 <HTML> <HEAD> <TITLE>Logiciels pour la biologie installs sur central</TITLE> <LINK REV="made" HREF="mailto:www@pasteur.fr"> <META NAME="Description" CONTENT="L'Institut Pasteur est un centre de recherche en biologie."> <META NAME="KeyWords" CONTENT="Pasteur, biologie"> <meta name="Author"    content="Pasteur Webmaster, www@pasteur.fr"> <meta name="Generator" content="WML 1.6.7 (02-08-1998)"> <meta name="Modified"  content="09-11-1998 15:35:20"> </HEAD> <BODY BGCOLOR="#FFFFFF" VLINK="#003399" LINK="#0033ff" TEXT="#000000"> <p align="center"> <a href="http://www.pasteur.fr/quoideneuf.html"><img align="bottom" border="0" src="http://www.pasteur.fr/icono/bouton-nouveau-s.gif" alt="Nouveaux"></a> <a href="http://www.pasteur.fr/search/"><img align="bottom" border="0" src="http://www.pasteur.fr/icono/bouton-recherche-s.gif" alt="Recherche"></a> <a href="http://www.pasteur.fr/guide.html"><img align="bottom" border="0" src="http://www.pasteur.fr/icono/bouton-guide-s.gif" alt="Guide"></a> </p> <H1 ALIGN="left"> <A HREF="http://www.pasteur.fr/"><IMG hspace="50" align="center" BORDER="0" SRC="http://www.pasteur.fr/icono/logopetit.gif" ALT=""></A> <font color="#003399">Logiciels pour la biologie installs sur central</font> </H1>  <hr> Dernire modification : 19 Mar 2003 18:49. <hr>  Pour chaque logiciel on donne les commandes Unix accessibles, les commandes Unix pour obtenir de l'aide, ainsi que les documents disponibles (fichiers PostScript, exemples d'utilisation, jeu d'essai, ...) fournis par les auteurs des programmes et prsents <i>tels quels</i>. La dernire version installe du logiciel est indique entre parenthses. Si le logiciel n'existe qu'en version X11, c'est indiqu par la mention [X11].  <hr>   <p> <ul>	  <li>	<h1>LISTE DES LOGICIELS</h1> <p> <dl>   	<dt>	<a name=ACNUC><i>ACNUC</i> (2003.01) 	<dd>	Recherche dans les banques de donnes : Genbank, EMBL, PIR/NBRF, Swissprot. Requtes complexes, traduction de gnes, extractions dans diffrents formats.[X11]   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>acnuc</td>      	<td><A HREF="/docs/man/doc/acnuc.1">man acnuc</a></td>    	</tr>  	<tr>    	<td>query</td>    	</tr>  	<tr>    	<td>query_win</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://pbil.univ-lyon1.fr/databases/acnuc.html">http://pbil.univ-lyon1.fr/databases/acnuc.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=ACT><i>act</i> (1.0) 	<dd>	DNA Sequence Comparison Viewer.[X11]   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>act</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www.sanger.ac.uk/Software/ACT/">http://www.sanger.ac.uk/Software/ACT/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=ALICE><i>Alice</i>  	<dd>	Motif discovery. The light version (-t) does not allow gaps.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>alice_nuc</td>    	</tr>  	<tr>    	<td>alice_nuc -t</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>alice_nuc -h</td></tr>      	<tr><td>alice_nuc -t -h</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>Beta version.</td>       </tr>         </table>  	<p>  	<dt>	<a name=ALSCRIPT><i>ALSCRIPT</i> (2.0) 	<dd>	Alignement de squences en PostScript.   Voir aussi : <a href="gensoft-algt.html#AMPS">AMPS</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>alscript</td>    	</tr>  	<tr>    	<td>alsnum</td>    	</tr>  	<tr>    	<td>clus2blc</td>    	</tr>  	<tr>    	<td>fast2blc</td>    	</tr>  	<tr>    	<td>msf2blc</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/alscript/alscript.ps">/local/gensoft/doc/alscript/alscript.ps</a></td></tr>      	<tr><td><A HREF="http://www-igbmc.u-strasbg.fr/BioInfo/alscript/front.html">http://www-igbmc.u-strasbg.fr/BioInfo/alscript/front.html</a></td></tr>      	<tr><td><A HREF="http://barton.ebi.ac.uk/manuals/alscript/alscript.html">http://barton.ebi.ac.uk/manuals/alscript/alscript.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=AMAS><i>AMAS</i> (1.67) 	<dd>	Analyse des proprits physico-chimiques des positions d'un alignement multiple (produits par AMPS).   Voir aussi : <a href="gensoft-algt.html#AMPS">AMPS</a>, <a href="gensoft-algt.html#ALSCRIPT">ALSCRIPT</a>, <a href="gensoft-algt.html#STAMP">STAMP</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>amas</td>      	<td><A HREF="/docs/man/doc/amas.1">man amas</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/amas/">/local/gensoft/doc/amas</a></td></tr>      	<tr><td><A HREF="http://barton.ebi.ac.uk/papers/amas/amas3d.html">http://barton.ebi.ac.uk/papers/amas/amas3d.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=AMPS><i>AMPS</i> (2.1) 	<dd>	Alignements multiples de protines.   Voir aussi : <a href="gensoft-algt.html#ALSCRIPT">ALSCRIPT</a>, <a href="gensoft-algt.html#AMAS">AMAS</a>, <a href="gensoft-algt.html#STAMP">STAMP</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>dayb</td>    	</tr>  	<tr>    	<td>makeampscom</td>    	</tr>  	<tr>    	<td>multalign</td>    	</tr>  	<tr>    	<td>order</td>    	</tr>  	<tr>    	<td>patt</td>    	</tr>  	<tr>    	<td>select</td>    	</tr>  	<tr>    	<td>sorter</td>    	</tr>  	<tr>    	<td>runamps</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td><A HREF="/docs/man/doc/amps.1">man amps</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/amps.html">AMPS</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://barton.ebi.ac.uk/manuals/amps/amps.html">http://barton.ebi.ac.uk/manuals/amps/amps.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=ANALYZE><i>ANALYZE</i> (95-10) 	<dd>	Statistiques sur les liaisons et/ou les liaisons desquilibres entre un locus de maladie et une  srie de loci de marqueurs (mthode 2-points).   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>analysis</td>    	</tr>  	<tr>    	<td>nonparametric</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td><A HREF="/docs/man/doc/analyze.1">man analyze</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/analyze//">/local/gensoft/doc/analyze/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=ARTEMIS><i>artemis</i> (4) 	<dd>	DNA sequence viewer and annotation tool[X11]   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>artemis</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/artemis//">/local/gensoft/doc/artemis/</a></td></tr>      	<tr><td><A HREF="http://www.sanger.ac.uk/Software/Artemis/stable/manual/">http://www.sanger.ac.uk/Software/Artemis/stable/manual/</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>Just type artemis to start.</td>       </tr>         </table>  	<p>  	<dt>	<a name=ASC><i>asc</i> (2.13) 	<dd>	The program package ASC / GM is designed for molecular-mechanical calculations in conjunction with surface computations. Version 2.1 has the following  options:  1) calculation of the surface of a set of intersecting spheres via the new    analytical method (the van-der-Waals surface     or the solvent-accessible surface with any probe radius) 2) numerical determination of the surface via the double cube lattice    method as well as the calculation of volume and of dot surfaces 3) computation of surface energies and hydrophilic/hydrophobic surface    for ensembles of molecules and their constituents    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>asc</td>      	<td>man asc</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/asc/">/local/gensoft/doc/asc</a></td></tr>    	</table>  	<p>  	<dt>	<a name=ASMG><i>Asmg</i> (970429) 	<dd>	Programme d'Assemblage de squences du TIGR  Voir aussi : <a href="gensoft-map.html#CONSED">Consed</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>asmg</td>      	<td><A HREF="/docs/man/doc/asmg.1">man asmg</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/Asmg//">/local/gensoft/doc/Asmg/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=ASPEX><i>aspex</i> (2.4) 	<dd>	Affected Sib Pair Exclusion Mapping   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>sib_ibd</td>    	</tr>  	<tr>    	<td>sib_tdt</td>    	</tr>  	<tr>    	<td>sib_phase</td>    	</tr>  	<tr>    	<td>sib_map</td>    	</tr>  	<tr>    	<td>sib_kin</td>    	</tr>  	<tr>    	<td>sib_clean</td>    	</tr>  	<tr>    	<td>list_incompat</td>    	</tr>  	<tr>    	<td>list_untyped</td>    	</tr>  	<tr>    	<td>xmgr_map</td>    	</tr>  	<tr>    	<td>rec_dist</td>    	</tr>  	<tr>    	<td>ligate</td>    	</tr>  	<tr>    	<td>restrict</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>man aspex</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/aspex/usage.html">http://bioweb.pasteur.fr/docs/aspex/usage.html</a></td></tr>      	<tr><td><A HREF="ftp://lahmed.stanford.edu/pub/aspex/index.html">ftp://lahmed.stanford.edu/pub/aspex/index.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=ASSP><i>ASSP</i>  	<dd>	(Accuracy of Secondary Structure Prediction) Prdit la prcision d'une prdiction de structure secondaire  partir d'un alignement multiple.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>assp</td>      	<td><A HREF="/docs/man/doc/assp.1">man assp</a></td>    	</tr>  	</table>  	<p>  	<dt>	<a name=BAMBE><i>bambe</i> (2.03b) 	<dd>	Bayesian Analysis in Molecular Biology and Evolution   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>bambe</td>    	</tr>  	<tr>    	<td>summarize</td>    	</tr>  	<tr>    	<td>remove-taxon</td>    	</tr>  	<tr>    	<td>meansd</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/bambe.html">bambe</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/bambe/">http://bioweb.pasteur.fr/docs/bambe/</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/bambe/">/local/gensoft/doc/bambe</a></td></tr>    	</table>  	<p>  	<dt>	<a name=BELVU><i>belvu</i> (2.9a) 	<dd>	View multiple alignments in good-looking colours.[X11]   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>belvu</td>      	<td>belvu</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www.cgr.ki.se/cgr/groups/sonnhammer/Belvu.html">http://www.cgr.ki.se/cgr/groups/sonnhammer/Belvu.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=BIONJ><i>BIONJ</i> (1) 	<dd>	Calcul d'arbre phylogntique par une version ameliore de l'algorithme NJ, adapate aux distances volutives obtenues  partir de squences alignes.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>bionj</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/bionj-simple.html">BIONJ</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www.crt.umontreal.ca/~olivierg/bionj.html">http://www.crt.umontreal.ca/~olivierg/bionj.html</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/bionj/bionj.ps">/local/gensoft/doc/bionj/bionj.ps</a></td></tr>    	</table>  	<p>  	<dt>	<a name=BIOPERL><i>Bioperl</i> (0.7.2) 	<dd>	Objets perl pour les squences, les  alignements, blast, et la phylognie   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>  	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>man bioperl</td></tr>      	<tr><td>man biostart</td></tr>      	<tr><td>man bptutorial</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://bio.perl.org/">http://bio.perl.org/</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/bioperl//">/local/gensoft/doc/bioperl/</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/bioperl/examples//">/local/gensoft/doc/bioperl/examples/</a></td></tr>      	<tr><td><A HREF="http://www.pasteur.fr/recherche/unites/sis/formation/bioperl/">http://www.pasteur.fr/recherche/unites/sis/formation/bioperl/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=BIOPYTHON><i>biopython</i> (1.00a4) 	<dd>	Python modules for sequences, alignements and other biological objects.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>  	</tr>  	<tr>  	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www.biopython.org/">http://www.biopython.org/</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/biopython/">/local/gensoft/doc/biopython</a></td></tr>    	</table>  	<p>  	<dt>	<a name=BIOTK><i>bioTk</i> (1.3) 	<dd>	a library of widgets and utilities (chromosome drawing, sequence scrolling window with annotations and      domains) designed to support the creation of graphical user interfaces in the domain of computational biology and      genome informatics (CBIL)   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>  	</tr>  	<tr>  	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/bioTk/">/local/gensoft/doc/bioTk</a></td></tr>    	</table>  	<p>  	<dt>	<a name=BIOTKPERL><i>bioTkperl</i> (0.8) 	<dd>	Toolkit graphique pour les squences.[X11]   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>bioTkperl</td>      	<td><A HREF="/docs/man/doc/bioTkperl.1">man bioTkperl</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/bioTkperl//">/local/gensoft/doc/bioTkperl/</a></td></tr>      	<tr><td><A HREF="http://www.cbil.upenn.edu/%7edsearls/bioTk.html">http://www.cbil.upenn.edu/%7edsearls/bioTk.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>bioTkperl est un "shell" perl. Les fichiers /local/gensoft/doc/bioTkperl/*TuT sont des exemples d'instructions perl pour crer des objets graphiques.</td>       </tr>         </table>  	<p>  	<dt>	<a name=BIOWISH><i>biowish</i> (1.1) 	<dd>	Molecular Biology related Tcl commands extension.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>xbbtools</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www.bioinformatics.org/~thomas/software/biowish/">http://www.bioinformatics.org/~thomas/software/biowish/</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/biowish/">/local/gensoft/doc/biowish</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>load /local/gensoft/lib/biowish/biowish.so </td>       </tr>         </table>  	<p>  	<dt>	<a name=BLAST2><i>BLAST2</i> (2.2.5) 	<dd>	Recherche de similarits entre une squence et les  squences d'une banque. Version multi-processeurs et avec gaps du NCBI.  Voir aussi : <a href="gensoft-algt.html#BLASTWU">blastwu</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>bl2seq</td>    	</tr>  	<tr>    	<td>blastall</td>    	</tr>  	<tr>    	<td>blastclust</td>    	</tr>  	<tr>    	<td>blastpgp</td>    	</tr>  	<tr>    	<td>copymat</td>    	</tr>  	<tr>    	<td>fastacmd</td>    	</tr>  	<tr>    	<td>fmerge</td>    	</tr>  	<tr>    	<td>formatdb</td>      	<td><A HREF="/docs/man/doc/formatdb.1">man formatdb</a></td>    	</tr>  	<tr>    	<td>impala</td>      	<td><A HREF="/docs/man/doc/impala.1">man impala</a></td>    	</tr>  	<tr>    	<td>makemat</td>    	</tr>  	<tr>    	<td>megablast</td>      	<td><A HREF="/docs/man/doc/megablast.1">man megablast</a></td>    	</tr>  	<tr>    	<td>rpsblast</td>      	<td><A HREF="/docs/man/doc/rpsblast.1">man rpsblast</a></td>    	</tr>  	<tr>    	<td>seedtop</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td><A HREF="/docs/man/doc/blast2.1">man blast2</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/blast2-simple.html">BLAST2</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www.ncbi.nlm.nih.gov/BLAST/">http://www.ncbi.nlm.nih.gov/BLAST/</a></td></tr>      	<tr><td><A HREF="http://www.ncbi.nlm.nih.gov/BLAST/tutorial/Altschul-2.html">http://www.ncbi.nlm.nih.gov/BLAST/tutorial/Altschul-2.html</a></td></tr>      	<tr><td><A HREF="http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/information3.html">http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/information3.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=BLASTOUTPUT><i>BlastOutput</i> (1) 	<dd>	API perl pour traiter les sorties Blast. Utilise optionellement bioperl.   Voir aussi : <a href="gensoft-prog.html#BIOPERL">Bioperl</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>  	</tr>  	<tr>  	</tr>  	</table>  	<p>  	<dt>	<a name=BLASTWU><i>blastwu</i> (2.0o) 	<dd>	Version 2 de blast de Washington University (avec gaps et multiprocesseurs).  Voir aussi : <a href="#BLAST2">Blast2</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>blastp</td>    	</tr>  	<tr>    	<td>blastn</td>    	</tr>  	<tr>    	<td>blastx</td>    	</tr>  	<tr>    	<td>tblastn</td>    	</tr>  	<tr>    	<td>tblastx</td>    	</tr>  	<tr>    	<td>xdformat</td>    	</tr>  	<tr>    	<td>xdget</td>    	</tr>  	<tr>    	<td>memfile</td>    	</tr>  	<tr>    	<td>sp2fasta</td>    	</tr>  	<tr>    	<td>gb2fasta</td>    	</tr>  	<tr>    	<td>gt2fasta</td>    	</tr>  	<tr>    	<td>pir2fasta</td>    	</tr>  	<tr>    	<td>pam</td>    	</tr>  	<tr>    	<td>nrdb</td>    	</tr>  	<tr>    	<td>patdb</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/wublast2.html">blastwu</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/blastwu//">/local/gensoft/doc/blastwu/</a></td></tr>      	<tr><td><A HREF="http://blast.wustl.edu/blast/README.html">http://blast.wustl.edu/blast/README.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=BLIMPS><i>BLIMPS</i> (3.5) 	<dd>	Recherche des blocs de la banque blocks dans une squence ou recherche d'un bloc dans une banque de squences. Des outils permettent d'analyser les rsultats.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>blalign</td>    	</tr>  	<tr>    	<td>blimps</td>      	<td><A HREF="/docs/man/doc/blimps.1">man blimps</a></td>    	</tr>  	<tr>    	<td>blimps.run</td>    	</tr>  	<tr>    	<td>blk2pssm</td>    	</tr>  	<tr>    	<td>blksort</td>    	</tr>  	<tr>    	<td>blweight</td>    	</tr>  	<tr>    	<td>codehop</td>    	</tr>  	<tr>    	<td>coduse</td>    	</tr>  	<tr>    	<td>getblock</td>    	</tr>  	<tr>    	<td>mablock</td>    	</tr>  	<tr>    	<td>multimat</td>    	</tr>  	<tr>    	<td>retblock</td>    	</tr>  	<tr>    	<td>bldist</td>    	</tr>  	<tr>    	<td>rank_matrix</td>    	</tr>  	<tr>    	<td>oligo_melt</td>    	</tr>  	<tr>    	<td>makeblockmap</td>    	</tr>  	<tr>    	<td>prints2blocks</td>    	</tr>  	<tr>    	<td>lisblk</td>    	</tr>  	<tr>    	<td>narrow</td>    	</tr>  	<tr>    	<td>blkprob</td>    	</tr>  	<tr>    	<td>blk2slx</td>    	</tr>  	<tr>    	<td>LAMA</td>    	</tr>  	<tr>    	<td>find_biassed_blocks</td>    	</tr>  	<tr>    	<td>fastaseqs</td>    	</tr>  	<tr>    	<td>addseqs</td>    	</tr>  	<tr>    	<td>cobbler</td>    	</tr>  	<tr>    	<td>interpro</td>    	</tr>  	<tr>    	<td>matrix_logob</td>    	</tr>  	<tr>    	<td>getseq</td>    	</tr>  	<tr>    	<td>motifj</td>    	</tr>  	<tr>    	<td>motomat</td>    	</tr>  	<tr>    	<td>uextract</td>    	</tr>  	<tr>    	<td>blastdat</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/motif/blimps-fr.html">BLIMPS</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www.blocks.fhcrc.org/help/help.html">http://www.blocks.fhcrc.org/help/help.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=BLIXEM><i>BLIXEM</i> (3.0) 	<dd>	(BLast matches In an X-windows Embedded Multiple Alignment) Affichage graphique des rsultats de BLAST aligns.[X11]  Voir aussi : <a href="gensoft-algt.html#MSPCRUNCH">MSPcrunch</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>blixem</td>      	<td><A HREF="/docs/man/doc/blixem.1">man blixem</a></td>    	</tr>  	<tr>    	<td>blixelect</td>    	</tr>  	</table>  	<p>  	<dt>	<a name=BLOCK><i>block</i> (1.0.1) 	<dd>	Analyse de liaisons pour de grandes familles (plusieurs milliers d'individus) avec la mthode d'chantillonage de Gibbs   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>block</td>      	<td><A HREF="/docs/man/doc/block.1">man block</a></td>    	</tr>  	<tr>    	<td>theta</td>      	<td><A HREF="/docs/man/doc/theta.1">man theta</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/block/peds//">/local/gensoft/doc/block/peds/</a></td></tr>      	<tr><td><A HREF="http://www.cs.auc.dk/~claus/block.html">http://www.cs.auc.dk/~claus/block.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=BLOSUM><i>blosum</i> (1992) 	<dd>	Gnration de matrices BLOSUM  partir de la banque Blocks.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>blosum</td>      	<td><A HREF="/docs/man/doc/blosum.1">man blosum</a></td>    	</tr>  	<tr>    	<td>matrix</td>    	</tr>  	<tr>    	<td>matalin</td>    	</tr>  	<tr>    	<td>matblas</td>    	</tr>  	<tr>    	<td>matfas</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/blocks/blosum//">/local/gensoft/doc/blocks/blosum/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=BOB><i>BOB</i> (1.04A) 	<dd>	(Blast Output Browser) Affichage des rsultats de Blast. [X11]  Voir aussi : <a href="gensoft-algt.html#TBOB">TBOB</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>bob</td>      	<td><A HREF="/docs/man/man/BoB.1.html">man BoB</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/bob/BoB.guide">/local/gensoft/doc/bob/BoB.guide</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/bob//">/local/gensoft/doc/bob/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=BOULDER><i>Boulder</i> (1.27) 	<dd>	A semantic free data interchange format. (contains Blast and Genbank parsers). XML input and output.  Voir aussi : <a href="gensoft-prog.html#BIOPERL">Bioperl</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>  	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>perldoc Boulder</td></tr>      	<tr><td>perldoc Boulder::XML</td></tr>      	<tr><td>perldoc Boulder::Genbank</td></tr>      	<tr><td>perldoc Boulder::Blast</td></tr>      	<tr><td>perldoc Boulder::Medline</td></tr>      	<tr><td>perldoc Boulder::Omim</td></tr>      	<tr><td>perldoc Boulder::Swissprot</td></tr>      	<tr><td>perldoc Boulder::Unigene</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://stein.cshl.org/software/boulder/">http://stein.cshl.org/software/boulder/</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/Boulder//">/local/gensoft/doc/Boulder/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=BOXSHADE><i>BOXSHADE</i> (3.33c) 	<dd>	Formattage d'alignements multiples.  Voir aussi : <a href="gensoft-algt.html#TEXSHADE">texshade</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>boxshade</td>      	<td><A HREF="/docs/man/doc/boxshade.1">man boxshade</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/boxshade.html">BOXSHADE</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/boxshade/">/local/gensoft/doc/boxshade</a></td></tr>      	<tr><td><A HREF="http://ludwig-sun1.unil.ch:8080/software/BOX_faq.html">http://ludwig-sun1.unil.ch:8080/software/BOX_faq.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=BTAB><i>BTAB</i> (5.01) 	<dd>	Analyse une sortie de Blast et produit un fichier tabul utilisable par des programmes comme BOB qui affichent les rsultats.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>btab</td>      	<td><A HREF="/docs/man/doc/btab.1">man btab</a></td>    	</tr>  	</table>  	<p>  	<dt>	<a name=CAP><i>cap</i> (3) 	<dd>	CAP3 Sequence Assembly Program   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>cap</td>      	<td><A HREF="/docs/man/doc/cap.1">man cap</a></td>    	</tr>  	</table>  	<p>  	<dt>	<a name=CASPAR><i>caspar</i>  	<dd>	CASPAR (Computerized Affected Sibling Pair Analyzer and Reporter) is an exploratory program to study the genetics of complex diseases.  It allows the user to explore hypotheses about how different factors  may be involved in disease susceptibility of polygenic diseases. It does multiple testing by simulating given data and measures significance of the results. CASPAR implements an extended form of Affected Sibling Pair (ASP) analysis.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>caspar</td>      	<td><A HREF="/docs/man/doc/caspar.1">man caspar</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/caspar/README.intro">/local/gensoft/doc/caspar/README.intro</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/caspar/README.methods">/local/gensoft/doc/caspar/README.methods</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/caspar/README.options">/local/gensoft/doc/caspar/README.options</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/caspar//">/local/gensoft/doc/caspar/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=CDS><i>CDS</i> (1) 	<dd>	Recherche de rgions codantes.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>cds</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>cds -h</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/cds-simple.html">CDS</a></td></tr>    	</table>  	<p>  	<dt>	<a name=CLUS2NEXUS><i>clus2nexus</i> (1) 	<dd>	convert an alignment in clustalw format to nexus format   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>clus2nexus</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>clus2nexus -help</td></tr>    	</table>  	<p>  	<dt>	<a name=CLUSTALW><i>CLUSTALW</i> (1.83) 	<dd>	Alignements de squences et phylognie.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>clustalw</td>      	<td><A HREF="/docs/man/doc/clustalw.1">man clustalw</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>clustalw -help</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/clustalw-simple.html">CLUSTALW</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://bess.u-strasbg.fr/BioInfo/ClustalW/">http://bess.u-strasbg.fr/BioInfo/ClustalW/</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/clustalw/README">/local/gensoft/doc/clustalw/README</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>Version Macintosh : <A HREF="ftp://ftp.pasteur.fr/pub/GenSoft/Macintosh/alignment/">ftp://ftp.pasteur.fr/pub/GenSoft/Macintosh/alignment/</A></td>       </tr>         </table>  	<p>  	<dt>	<a name=CLUSTALX><i>ClustalX</i> (1.83) 	<dd>	Version Graphique de Clustal[X11]   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>clustalx</td>      	<td><A HREF="/docs/man/doc/clustalx.1">man clustalx</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://bess.u-strasbg.fr/BioInfo/ClustalX/">http://bess.u-strasbg.fr/BioInfo/ClustalX/</a></td></tr>      	<tr><td><A HREF="/docs/clustalx/">http://bioweb.pasteur.fr/docs/clustalx/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=CLUSTER><i>CLUSTER</i> (2.0) 	<dd>	Classification.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>cluster</td>      	<td><A HREF="/docs/man/doc/cluster.1">man cluster</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/cluster/">/local/gensoft/doc/cluster</a></td></tr>    	</table>  	<p>  	<dt>	<a name=CN3D><i>Cn3D</i> (3.00) 	<dd>	See in 3D - Structure Viewer[X11]   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>Cn3D</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml">http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml</a></td></tr>    	</table>  	<p>  	<dt>	<a name=CODEGEN><i>CodeGen</i>  	<dd>	Module perl pour le code genetique.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>  	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>perldoc Gensoft::CodeGen</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>use Gensoft::CodeGen;</td>       </tr>         </table>  	<p>  	<dt>	<a name=CODNOCOD><i>CODNOCOD</i> (1) 	<dd>	Reads genbank format sequence entries and outputs various  features.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>codnocod</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>codnocod -h</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/codnocod.html">CODNOCOD</a></td></tr>    	</table>  	<p>  	<dt>	<a name=CODONTREE><i>CODONTREE</i> (1.1) 	<dd>	Analyse des proprits de rgions codantes : usage  des codons, composition en bases, matrice de distances.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>codontree</td>      	<td><A HREF="/docs/man/doc/codontree.1">man codontree</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/codontree.html">CODONTREE</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/codontree//">/local/gensoft/doc/codontree/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=CODONW><i>CodonW</i> (1.4.2) 	<dd>	CodonW is a package for codon usage analysis. Multivariate Analysis (MVA) of codon usage.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>codonw</td>      	<td><A HREF="/docs/man/doc/codonw.1">man codonw</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>codonw -h</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/codonw.html">CodonW</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/codonW/">/local/gensoft/doc/codonW</a></td></tr>      	<tr><td><A HREF="http://www.molbiol.ox.ac.uk/cu/">http://www.molbiol.ox.ac.uk/cu/</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>Un fichier de donnes pour test est disponible:  /local/gensoft/doc/codonW/input.dat</td>       </tr>         </table>  	<p>  	<dt>	<a name=COMALIGN><i>ComAlign</i> (1) 	<dd>	Combining many multiple alignments in one improved alignment.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>ComAlign</td>    	</tr>  	<tr>    	<td>DNAgen</td>    	</tr>  	<tr>    	<td>ProfAlign</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>ComAlign -h</td></tr>      	<tr><td>DNAgen -h</td></tr>      	<tr><td>ProfAlign -h</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/comalign.html">ComAlign</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/ComAlign/">/local/gensoft/doc/ComAlign</a></td></tr>      	<tr><td><A HREF="http://www.daimi.au.dk/~ocaprani/ComAlign/ComAlign.html">http://www.daimi.au.dk/~ocaprani/ComAlign/ComAlign.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=COMBAT><i>combat</i> (1.0) 	<dd>	COMBined AlignmenT: Comparison of coding DNA   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>combat</td>      	<td><A HREF="/docs/man/doc/combat.1">man combat</a></td>    	</tr>  	<tr>    	<td>combat_combine</td>    	</tr>  	<tr>    	<td>combat_convert</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/combat.html">combat</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/combat//">/local/gensoft/doc/combat/</a></td></tr>      	<tr><td><A HREF="http://www.daimi.au.dk/~cstorm/combat/">http://www.daimi.au.dk/~cstorm/combat/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=CONFMAT><i>confmat</i> (1) 	<dd>	CONFMAT calculates the sidechain conformational matrix of a protein : based on the conformation of the backbone, it provides the probabilities that each possible rotamer can be accomodated for each residue in the protein. The rotamer with the highest probability can be used as a model of the  conformation of the corresponding side-chain. In addition, a crude estimate of the conformational entropy of each residue can be derived from the  conformational matrix, using information theory.  Voir aussi : <a href="gensoft-aa.html#ENVIRON">environ</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>confmat</td>      	<td><A HREF="/docs/man/doc/confmat.1">man confmat</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/confmat-simple.html">confmat</a></td></tr>    	</table>  	<p>  	<dt>	<a name=CONSED><i>Consed</i> (11.0) 	<dd>	Editeur de contigs assembls par phredPhrap.[X11]  Voir aussi : <a href="gensoft-map.html#PHRED">Phred</a>, <a href="gensoft-map.html#PHRAP">Phrap</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>phredPhrap</td>      	<td><A HREF="/docs/man/doc/phredPhrap.1">man phredPhrap</a></td>    	</tr>  	<tr>    	<td>consed</td>      	<td><A HREF="/docs/man/doc/consed.1">man consed</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://bozeman.genome.washington.edu/consed/consed.html">http://bozeman.genome.washington.edu/consed/consed.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=CONSENSUS><i>consensus</i> (1.9e) 	<dd>	Identification of consensus patterns in unaligned DNA and protein sequences (G.Z. Hertz).   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>con-filter</td>    	</tr>  	<tr>    	<td>consensus</td>      	<td><A HREF="/docs/man/doc/consensus.1">man consensus</a></td>    	</tr>  	<tr>    	<td>fasta-consensus</td>    	</tr>  	<tr>    	<td>gcg-consensus</td>    	</tr>  	<tr>    	<td>genbank-consensus</td>    	</tr>  	<tr>    	<td>gmat-inf-gc</td>    	</tr>  	<tr>    	<td>make-matrix</td>    	</tr>  	<tr>    	<td>p-value</td>    	</tr>  	<tr>    	<td>patser</td>    	</tr>  	<tr>    	<td>rand-seqs</td>    	</tr>  	<tr>    	<td>seq-modifier</td>    	</tr>  	<tr>    	<td>wconsensus</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>patser -h</td></tr>      	<tr><td>patser -help</td></tr>      	<tr><td>wconsensus -h</td></tr>      	<tr><td>wconsensus -help</td></tr>      	<tr><td>p-value -h</td></tr>      	<tr><td>consensus -h</td></tr>      	<tr><td>consensus -help</td></tr>      	<tr><td>gcg-consensus -h</td></tr>      	<tr><td>con-filter -h</td></tr>      	<tr><td>con-filter -help</td></tr>      	<tr><td>fasta-consensus -h</td></tr>      	<tr><td>make-matrix -h</td></tr>      	<tr><td>gmat-inf-gc -h</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/consensus-simple.html">consensus</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/consensus/">/local/gensoft/doc/consensus</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>consensus-matrix (home made) may help you to extract the matrix from the (w)consensus output</td>       </tr>         </table>  	<p>  	<dt>	<a name=CONSINSPECTOR><i>ConsInspector</i> (3.3) 	<dd>	ConsInspector recherche des sites de liaison dans une squence d'acides  nucliques par comparaison avec des squences consensus.   Voir aussi : <a href="gensoft-na.html#MATINSPECTOR">MatInspector</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>consinspector</td>      	<td><A HREF="/docs/man/doc/consinspector.1">man consinspector</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www.gsf.de/biodv/consinspector.html">http://www.gsf.de/biodv/consinspector.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=CORESEARCH><i>CoreSearch</i> (1.3) 	<dd>	Identification d'lments consensus dans un ensemble de squences d'ADN non alignes.   Voir aussi : <a href="gensoft-na.html#CONSINSPECTOR">ConsInspector</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>coresearch</td>      	<td><A HREF="/docs/man/doc/coresearch.1">man coresearch</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www.gsf.de/biodv/coresearch.html">http://www.gsf.de/biodv/coresearch.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=COVE><i>COVE</i> (2.4.4) 	<dd>	Modles de covariance de familles d'ARN : gnration de modles (covet), alignement (covea), recherche dans une banque (covels), prdiction d'une structure (coves).   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>covea</td>    	</tr>  	<tr>    	<td>coveb</td>    	</tr>  	<tr>    	<td>covee</td>    	</tr>  	<tr>    	<td>covels</td>    	</tr>  	<tr>    	<td>coves</td>    	</tr>  	<tr>    	<td>covet</td>    	</tr>  	<tr>    	<td>structcheck</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td><A HREF="/docs/man/doc/cove.1">man cove</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/cove/Guide.ps">/local/gensoft/doc/cove/Guide.ps</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/cove/Demos/">/local/gensoft/doc/cove/Demos</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/cove/RNA_cove_models.ps">/local/gensoft/doc/cove/RNA_cove_models.ps</a></td></tr>    	</table>  	<p>  	<dt>	<a name=CRIMAP><i>CRI-MAP</i> (2.4) 	<dd>	Construction de cartes de liaison multi-locus.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>crimap</td>      	<td><A HREF="/docs/man/man/crimap.1.html">man crimap</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://linkage.rockefeller.edu/soft/crimap/">http://linkage.rockefeller.edu/soft/crimap/</a></td></tr>      	<tr><td><A HREF="http://biobase.dk/Embnetut/Crimap/index.html">http://biobase.dk/Embnetut/Crimap/index.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=CSR><i>CSR</i> (1) 	<dd>	Maximal Common 3D Substructure Searching with the Combined SDM/RMS (CSR) Algorithm, Comput. Chem. 1998,22[6],463-465. M.Petitjean   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>CSR</td>      	<td><A HREF="/docs/man/doc/CSR.1">man CSR</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/CSR.html">CSR</a></td></tr>    	</table>  	<p>  	<dt>	<a name=DARWIN><i>DARWIN</i> (2.1a) 	<dd>	(Data Analysis and Retrieval With Indexed Nucleotide/peptide squences) Langage de programmation interprt pour l'analyse de squences.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>darwin</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/darwin/darwin.ps">/local/gensoft/doc/darwin/darwin.ps</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/darwin//">/local/gensoft/doc/darwin/</a></td></tr>      	<tr><td><A HREF="http://cbrg.inf.ethz.ch/">http://cbrg.inf.ethz.ch/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=DBWATCHER><i>DBWatcher</i> (2.00) 	<dd>	Soumission priodique de squences par Blast, en fonction des mises  jour des banques (locales). [X11]  Voir aussi : <a href="gensoft-algt.html#FASTALERT">FASTALERT</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>setdbwatcher</td>      	<td><A HREF="/docs/man/doc/setdbwatcher.1">man setdbwatcher</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td><A HREF="/docs/man/doc/dbwatcher.1">man dbwatcher</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www-igbmc.u-strasbg.fr/BioInfo/LocalDoc/DBWatcher/">http://www-igbmc.u-strasbg.fr/BioInfo/LocalDoc/DBWatcher/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=DCA><i>dca</i> (1.1) 	<dd>	Alignement multiple simultane de sequences d'acides nucleiques ou de proteines   Voir aussi : <a href="#MSA">msa</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>dca</td>      	<td><A HREF="/docs/man/doc/dca.1">man dca</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/dca-simple.html">dca</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://bibiserv.TechFak.Uni-Bielefeld.DE/dca/">http://bibiserv.TechFak.Uni-Bielefeld.DE/dca/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=DECORATE><i>decorate</i>  	<dd>	DECORATE will use the coordinates of the main chain of the template PDB file and generate 3D-coordinates of all sides chains specified by the gapless alignement provided on input.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>decorate</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/decorate.html">decorate</a></td></tr>    	</table>  	<p>  	<dt>	<a name=DIALIGN><i>DIALIGN</i> (2.2.1) 	<dd>	Alignement multiple de squence (ADN ou protine) par comparaisons segment par segment.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>dialign</td>      	<td><A HREF="/docs/man/doc/dialign.1">man dialign</a></td>    	</tr>  	<tr>    	<td>dialign2</td>      	<td><A HREF="/docs/man/doc/dialign2.1">man dialign2</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/dialign2-simple.html">DIALIGN</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/dialign2//">/local/gensoft/doc/dialign2/</a></td></tr>      	<tr><td><A HREF="http://bibiserv.techfak.uni-bielefeld.de/dialign/">http://bibiserv.techfak.uni-bielefeld.de/dialign/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=DIANA><i>Diana</i>  	<dd>	Analyse d'ADN, recherche de gnes.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>  	</tr>  	<tr>  	</tr>  	</table>  	<p>  	<dt>	<a name=DINAMO><i>dinamo</i> (1.0) 	<dd>	A Coupled Sequence Alignment Editor/Molecular Graphics Tool For Comparative Modeling and Threading of Proteins   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>dinamo</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/dinamo/">http://bioweb.pasteur.fr/docs/dinamo/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=DNA2PROTAL><i>dna2protal</i> (1) 	<dd>	Translates a DNA alignment, with gaps, into its protein equivalent.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>dna2protal</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>dna2protal -h</td></tr>    	</table>  	<p>  	<dt>	<a name=DNAP><i>dnap</i> (1) 	<dd>	Check whether a sequence is DNA.  Voir aussi : <a href="gensoft-prog.html#SEQUTILS">SeqUtils</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>dnap</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>dnap -h</td></tr>    	</table>  	<p>  	<dt>	<a name=DOTTER><i>DOTTER</i> (3.1) 	<dd>	Dotplots (matrices de points) avec amlioration  de la visualisation.[X11]   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>dotter</td>      	<td><A HREF="/docs/man/doc/dotter.1">man dotter</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www.cgr.ki.se/cgr/groups/sonnhammer/Dotter.html">http://www.cgr.ki.se/cgr/groups/sonnhammer/Dotter.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=DRAWSEQ><i>drawseq</i> (1.0) 	<dd>	Draw pretty views of biosequences.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>drawseq</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>drawseq help</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/drawseq/">http://bioweb.pasteur.fr/docs/drawseq/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=DRUID><i>druid</i> (1.0) 	<dd>	Localization of recombination breakpoints in an alignment of sequences   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>druid</td>      	<td><A HREF="/docs/man/doc/druid.1">man druid</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/druid.html">druid</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/Druid//">/local/gensoft/doc/Druid/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=DSC><i>DSC</i> (1.2) 	<dd>	(Discrimination of protein Secondary structure Class) Prdiction de structure secondaire (3 tats)  partir  d'un alignement avec une prcision d'environ 70%.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>dsc</td>      	<td><A HREF="/docs/man/doc/dsc.1">man dsc</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/dsc-simple.html">DSC</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www.lif.icnet.uk/bmm/dsc/manual.html">http://www.lif.icnet.uk/bmm/dsc/manual.html</a></td></tr>      	<tr><td><A HREF="http://bonsai.lif.icnet.uk/bmm/dsc/dsc_form_align.html">http://bonsai.lif.icnet.uk/bmm/dsc/dsc_form_align.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=DSSP><i>DSSP</i> (July 1995) 	<dd>	Dfinition d'une structure secondaire  l'aide des coordonnes 3D d'une entre de PDB.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>dssp</td>      	<td><A HREF="/docs/man/doc/dssp.1">man dssp</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/dssp-simple.html">DSSP</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/dssp/">/local/gensoft/doc/dssp</a></td></tr>      	<tr><td><A HREF="http://www.sander.embl-heidelberg.de/dssp/descrip.html">http://www.sander.embl-heidelberg.de/dssp/descrip.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=DYNAMITE><i>DYNAMITE</i> (1.3a) 	<dd>	Dynamite is a code generating language developed for sequence comparison methods by dynamic programming.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>dyc</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/dynamite/makefile">/local/gensoft/doc/dynamite/makefile</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/dynamite/dynamite.ps">/local/gensoft/doc/dynamite/dynamite.ps</a></td></tr>      	<tr><td><A HREF="http://www.sanger.ac.uk/Software/Dynamite">http://www.sanger.ac.uk/Software/Dynamite</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>Please, see the makefile for local settings. </td>       </tr>         </table>  	<p>  	<dt>	<a name=EFETCH><i>EFETCH</i>  	<dd>	Recherche dans les banques sur Accession Number ou Entry name.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>efetch</td>      	<td>man efetch</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="http://central.pasteur.fr/seqanal/interfaces/efetch-simple.html">EFETCH</a></td></tr>    	</table>  	<p>  	<dt>	<a name=EMBOSS><i>EMBOSS</i> (2.3.1) 	<dd>	European Molecular Biology Open Software Suite[X11]   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>abiview</td>    	</tr>  	<tr>    	<td>acdc</td>    	</tr>  	<tr>    	<td>alignwrap</td>    	</tr>  	<tr>    	<td>antigenic</td>    	</tr>  	<tr>    	<td>backtranseq</td>    	</tr>  	<tr>    	<td>banana</td>    	</tr>  	<tr>    	<td>biosed</td>    	</tr>  	<tr>    	<td>btwisted</td>    	</tr>  	<tr>    	<td>cai</td>    	</tr>  	<tr>    	<td>chaos</td>    	</tr>  	<tr>    	<td>charge</td>    	</tr>  	<tr>    	<td>checktrans</td>    	</tr>  	<tr>    	<td>chips</td>    	</tr>  	<tr>    	<td>cirdna</td>    	</tr>  	<tr>    	<td>codcmp</td>    	</tr>  	<tr>    	<td>coderet</td>    	</tr>  	<tr>    	<td>compseq</td>    	</tr>  	<tr>    	<td>cons</td>    	</tr>  	<tr>    	<td>contacts</td>    	</tr>  	<tr>    	<td>cpgplot</td>    	</tr>  	<tr>    	<td>cpgreport</td>    	</tr>  	<tr>    	<td>cusp</td>    	</tr>  	<tr>    	<td>cutgextract</td>    	</tr>  	<tr>    	<td>cutseq</td>    	</tr>  	<tr>    	<td>dan</td>    	</tr>  	<tr>    	<td>dbiblast</td>    	</tr>  	<tr>    	<td>dbifasta</td>    	</tr>  	<tr>    	<td>dbiflat</td>    	</tr>  	<tr>    	<td>dbigcg</td>    	</tr>  	<tr>    	<td>degapseq</td>    	</tr>  	<tr>    	<td>descseq</td>    	</tr>  	<tr>    	<td>dichet</td>    	</tr>  	<tr>    	<td>diffseq</td>    	</tr>  	<tr>    	<td>digest</td>    	</tr>  	<tr>    	<td>distmat</td>    	</tr>  	<tr>    	<td>domainer</td>    	</tr>  	<tr>    	<td>dotmatcher</td>    	</tr>  	<tr>    	<td>dotpath</td>    	</tr>  	<tr>    	<td>dottup</td>    	</tr>  	<tr>    	<td>dreg</td>    	</tr>  	<tr>    	<td>einverted</td>    	</tr>  	<tr>    	<td>embossdata</td>    	</tr>  	<tr>    	<td>embossversion</td>    	</tr>  	<tr>    	<td>emma</td>    	</tr>  	<tr>    	<td>emowse</td>    	</tr>  	<tr>    	<td>entret</td>    	</tr>  	<tr>    	<td>eprimer3</td>    	</tr>  	<tr>    	<td>equicktandem</td>    	</tr>  	<tr>    	<td>est2genome</td>    	</tr>  	<tr>    	<td>etandem</td>    	</tr>  	<tr>    	<td>extractfeat</td>    	</tr>  	<tr>    	<td>extractseq</td>    	</tr>  	<tr>    	<td>findkm</td>    	</tr>  	<tr>    	<td>freak</td>    	</tr>  	<tr>    	<td>fuzznuc</td>    	</tr>  	<tr>    	<td>fuzzpro</td>    	</tr>  	<tr>    	<td>fuzztran</td>    	</tr>  	<tr>    	<td>garnier</td>    	</tr>  	<tr>    	<td>geecee</td>    	</tr>  	<tr>    	<td>getorf</td>    	</tr>  	<tr>    	<td>helixturnhelix</td>    	</tr>  	<tr>    	<td>hmoment</td>    	</tr>  	<tr>    	<td>iep</td>    	</tr>  	<tr>    	<td>infoalign</td>    	</tr>  	<tr>    	<td>infoseq</td>    	</tr>  	<tr>    	<td>interface</td>    	</tr>  	<tr>    	<td>isochore</td>    	</tr>  	<tr>    	<td>jembossctl</td>    	</tr>  	<tr>    	<td>lindna</td>    	</tr>  	<tr>    	<td>listor</td>    	</tr>  	<tr>    	<td>marscan</td>    	</tr>  	<tr>    	<td>maskfeat</td>    	</tr>  	<tr>    	<td>maskseq</td>    	</tr>  	<tr>    	<td>matcher</td>    	</tr>  	<tr>    	<td>megamerger</td>    	</tr>  	<tr>    	<td>merger</td>    	</tr>  	<tr>    	<td>msbar</td>    	</tr>  	<tr>    	<td>mwfilter</td>    	</tr>  	<tr>    	<td>needle</td>    	</tr>  	<tr>    	<td>newcpgreport</td>    	</tr>  	<tr>    	<td>newcpgseek</td>    	</tr>  	<tr>    	<td>newseq</td>    	</tr>  	<tr>    	<td>noreturn</td>    	</tr>  	<tr>    	<td>notseq</td>    	</tr>  	<tr>    	<td>nrscope</td>    	</tr>  	<tr>    	<td>nthseq</td>    	</tr>  	<tr>    	<td>octanol</td>    	</tr>  	<tr>    	<td>oddcomp</td>    	</tr>  	<tr>    	<td>palindrome</td>    	</tr>  	<tr>    	<td>pasteseq</td>    	</tr>  	<tr>    	<td>patmatdb</td>    	</tr>  	<tr>    	<td>patmatmotifs</td>    	</tr>  	<tr>    	<td>pdbtosp</td>    	</tr>  	<tr>    	<td>pepcoil</td>    	</tr>  	<tr>    	<td>pepinfo</td>    	</tr>  	<tr>    	<td>pepnet</td>    	</tr>  	<tr>    	<td>pepstats</td>    	</tr>  	<tr>    	<td>pepwheel</td>    	</tr>  	<tr>    	<td>pepwindow</td>    	</tr>  	<tr>    	<td>pepwindowall</td>    	</tr>  	<tr>    	<td>plotcon</td>    	</tr>  	<tr>    	<td>plotorf</td>    	</tr>  	<tr>    	<td>polydot</td>    	</tr>  	<tr>    	<td>preg</td>    	</tr>  	<tr>    	<td>prettyplot</td>    	</tr>  	<tr>    	<td>prettyseq</td>    	</tr>  	<tr>    	<td>primersearch</td>    	</tr>  	<tr>    	<td>printsextract</td>    	</tr>  	<tr>    	<td>profit</td>    	</tr>  	<tr>    	<td>prophecy</td>    	</tr>  	<tr>    	<td>prophet</td>    	</tr>  	<tr>    	<td>prosextract</td>    	</tr>  	<tr>    	<td>pscan</td>    	</tr>  	<tr>    	<td>psiblasts</td>    	</tr>  	<tr>    	<td>rebaseextract</td>    	</tr>  	<tr>    	<td>recoder</td>    	</tr>  	<tr>    	<td>redata</td>    	</tr>  	<tr>    	<td>remap</td>    	</tr>  	<tr>    	<td>restover</td>    	</tr>  	<tr>    	<td>restrict</td>    	</tr>  	<tr>    	<td>revseq</td>    	</tr>  	<tr>    	<td>scopalign</td>    	</tr>  	<tr>    	<td>scope</td>    	</tr>  	<tr>    	<td>scopparse</td>    	</tr>  	<tr>    	<td>seealso</td>    	</tr>  	<tr>    	<td>seqmatchall</td>    	</tr>  	<tr>    	<td>seqnr</td>    	</tr>  	<tr>    	<td>seqret</td>    	</tr>  	<tr>    	<td>seqretsplit</td>    	</tr>  	<tr>    	<td>seqsort</td>    	</tr>  	<tr>    	<td>showalign</td>    	</tr>  	<tr>    	<td>showdb</td>    	</tr>  	<tr>    	<td>showfeat</td>    	</tr>  	<tr>    	<td>showorf</td>    	</tr>  	<tr>    	<td>showseq</td>    	</tr>  	<tr>    	<td>shuffleseq</td>    	</tr>  	<tr>    	<td>sigcleave</td>    	</tr>  	<tr>    	<td>siggen</td>    	</tr>  	<tr>    	<td>sigscan</td>    	</tr>  	<tr>    	<td>silent</td>    	</tr>  	<tr>    	<td>splitter</td>    	</tr>  	<tr>    	<td>stretcher</td>    	</tr>  	<tr>    	<td>stssearch</td>    	</tr>  	<tr>    	<td>supermatcher</td>    	</tr>  	<tr>    	<td>swissparse</td>    	</tr>  	<tr>    	<td>syco</td>    	</tr>  	<tr>    	<td>textsearch</td>    	</tr>  	<tr>    	<td>tfextract</td>    	</tr>  	<tr>    	<td>tfm</td>    	</tr>  	<tr>    	<td>tfscan</td>    	</tr>  	<tr>    	<td>tmap</td>    	</tr>  	<tr>    	<td>transeq</td>    	</tr>  	<tr>    	<td>trimest</td>    	</tr>  	<tr>    	<td>trimseq</td>    	</tr>  	<tr>    	<td>vectorstrip</td>    	</tr>  	<tr>    	<td>water</td>    	</tr>  	<tr>    	<td>whichdb</td>    	</tr>  	<tr>    	<td>wobble</td>    	</tr>  	<tr>    	<td>wordcount</td>    	</tr>  	<tr>    	<td>wordmatch</td>    	</tr>  	<tr>    	<td>wossname</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="http://www.pasteur.fr/cgi-bin/biology/bnb_s.pl?query=EMBOSS">EMBOSS</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/EMBOSS/">http://bioweb.pasteur.fr/docs/EMBOSS/</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/EMBOSS/doc/">http://bioweb.pasteur.fr/docs/doc-gensoft/EMBOSS/doc/</a></td></tr>      	<tr><td><A HREF="http://www.uk.embnet.org/Software/EMBOSS/">http://www.uk.embnet.org/Software/EMBOSS/</a></td></tr>      	<tr><td><A HREF="http://www.uk.embnet.org/Software/EMBOSS/Apps/">http://www.uk.embnet.org/Software/EMBOSS/Apps/</a></td></tr>      	<tr><td><A HREF="http://www.uk.embnet.org/Software/EMBOSS/Doc/Tutorial/">http://www.uk.embnet.org/Software/EMBOSS/Doc/Tutorial/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=ENVIRON><i>environ</i> (1) 	<dd>	ENVIRON is a program designed to calculate accessible as well as  buried surface area, using the method described originally by Shrake and Rupley, as well as to calculate a free energy of 'environment', i.e. a semi-empiricall attempt to quantify the hydrophobic interactions, following a model originally described by Eisenberg and McLachlan.  Voir aussi : <a href="gensoft-aa.html#CONFMAT">confmat</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>environ</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>man 1 environ</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/environ-simple.html">environ</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/environ/manual.txt">/local/gensoft/doc/environ/manual.txt</a></td></tr>    	</table>  	<p>  	<dt>	<a name=ESPRIPT><i>ESPript</i> (1.9) 	<dd>	ESPript is a utility to generate a pretty PostScript output from  aligned sequences.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>ESPript</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/docs/ESPript/">ESPript</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/ESPript/">http://bioweb.pasteur.fr/docs/ESPript/</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/ESPript/">/local/gensoft/doc/ESPript</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>Click on "Execute wwwESPript NOW" on the Web page to execute ESPript.</td>       </tr>         </table>  	<p>  	<dt>	<a name=ESTATE><i>ESTate</i> (0.5.0) 	<dd>	Expressed Sequence Tag Analysis Tools Etc   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>alignsearch</td>    	</tr>  	<tr>    	<td>calcwordprob</td>      	<td><A HREF="/docs/man/man/calcwordprob.1.html">man calcwordprob</a></td>    	</tr>  	<tr>    	<td>estcluster</td>      	<td><A HREF="/docs/man/man/estcluster.1.html">man estcluster</a></td>    	</tr>  	<tr>    	<td>fasta2usage</td>      	<td><A HREF="/docs/man/man/fasta2usage.1.html">man fasta2usage</a></td>    	</tr>  	<tr>    	<td>flat2coding</td>      	<td><A HREF="/docs/man/man/flat2coding.1.html">man flat2coding</a></td>    	</tr>  	<tr>    	<td>framefinder</td>      	<td><A HREF="/docs/man/man/framefinder.1.html">man framefinder</a></td>    	</tr>  	<tr>    	<td>precluster</td>      	<td><A HREF="/docs/man/man/precluster.1.html">man precluster</a></td>    	</tr>  	<tr>    	<td>revcomp</td>    	</tr>  	<tr>    	<td>vpbuild</td>      	<td><A HREF="/docs/man/man/vpbuild.1.html">man vpbuild</a></td>    	</tr>  	<tr>    	<td>vpsearch</td>      	<td><A HREF="/docs/man/man/vpsearch.1.html">man vpsearch</a></td>    	</tr>  	<tr>    	<td>wordsearch</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td><A HREF="/docs/man/man/ESTate.1.html">man ESTate</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www.hgmp.mrc.ac.uk/~gslater/ESTate/">http://www.hgmp.mrc.ac.uk/~gslater/ESTate/</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/ESTate/">/local/gensoft/doc/ESTate</a></td></tr>    	</table>  	<p>  	<dt>	<a name=EXTRACTCDS><i>extractcds</i> (1.0) 	<dd>	Extracts translation(s) from an Embl or Genbank entry   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>extractcds</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>extractcds -h</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/extractcds.html">extractcds</a></td></tr>    	</table>  	<p>  	<dt>	<a name=FASTA><i>FASTA</i> (34t21b0) 	<dd>	Fasta permet de rechercher des similarits entre une squence et les squences d'une banque.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>map_db</td>      	<td><A HREF="/docs/man/man/map_db.1.html">man map_db</a></td>    	</tr>  	<tr>    	<td>fasta</td>      	<td><A HREF="/docs/man/man/fasta.1.html">man fasta</a></td>    	</tr>  	<tr>    	<td>ssearch</td>      	<td>man ssearch</td>    	</tr>  	<tr>    	<td>prss</td>      	<td><A HREF="/docs/man/man/prss.1.html">man prss</a></td>    	</tr>  	<tr>    	<td>fastf</td>      	<td><A HREF="/docs/man/man/fastf.1.html">man fastf</a></td>    	</tr>  	<tr>    	<td>fasts</td>      	<td><A HREF="/docs/man/man/fasts.1.html">man fasts</a></td>    	</tr>  	<tr>    	<td>tfastf</td>    	</tr>  	<tr>    	<td>tfasta</td>    	</tr>  	<tr>    	<td>fastx</td>    	</tr>  	<tr>    	<td>tfastx</td>    	</tr>  	<tr>    	<td>fasty</td>    	</tr>  	<tr>    	<td>tfasty</td>    	</tr>  	<tr>    	<td>tfasts</td>    	</tr>  	<tr>    	<td>ssearch_t</td>    	</tr>  	<tr>    	<td>fasta_t</td>    	</tr>  	<tr>    	<td>fastf_t</td>    	</tr>  	<tr>    	<td>fasts_t</td>    	</tr>  	<tr>    	<td>tfastf_t</td>    	</tr>  	<tr>    	<td>tfasta_t</td>    	</tr>  	<tr>    	<td>fastx_t</td>    	</tr>  	<tr>    	<td>tfastx_t</td>    	</tr>  	<tr>    	<td>fasty_t</td>    	</tr>  	<tr>    	<td>tfasty_t</td>    	</tr>  	<tr>    	<td>tfasts_t</td>    	</tr>  	<tr>    	<td>fastm</td>    	</tr>  	<tr>    	<td>fastm_t</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td><A HREF="/docs/man/man/pvcomp.1.html">man pvcomp</a></td></tr>      	<tr><td><A HREF="/docs/man/man/align.1.html">man align</a></td></tr>      	<tr><td><A HREF="/docs/man/man/lalign.1.html">man lalign</a></td></tr>      	<tr><td><A HREF="/docs/man/man/prdf.1.html">man prdf</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/fasta-simple.html">FASTA</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/fasta//">/local/gensoft/doc/fasta/</a></td></tr>      	<tr><td><A HREF="http://www.pasteur.fr/cgi-bin/biology/bnb_s.pl?english=1&bool=et&query=fasta&bio=analyse+de+squences">http://www.pasteur.fr/cgi-bin/biology/bnb_s.pl?english=1&bool=et&query=fasta&bio=analyse+de+squences</a></td></tr>      	<tr><td><A HREF="http://alpha10.bioch.virginia.edu/fasta/">http://alpha10.bioch.virginia.edu/fasta/</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>Les version 3 et 3_t sont equivalentes du point de vue de la fonction, la version 3_t est multi-processeurs (c'est la version utilisee par l'interface Web). Les programmes align, lfasta, etc... qui ne comporte pas le chiffre 3 font partie de l'ancienne distribution de fasta et ne sont pas repris dans la version 3.</td>       </tr>         </table>  	<p>  	<dt>	<a name=FASTALERT><i>FASTALERT</i> (v1.0) 	<dd>	Lancements priodiques automatiques de fasta sur une squence requte pour revaluer les rsultats au fur et  mesure des mises  jour des banques.   Voir aussi : <a href="gensoft-algt.html#DBWATCHER">DBWatcher</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>facust</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td><A HREF="/docs/man/doc/fastalert.1">man fastalert</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>La version actuelle n'est plus  jour. Mise  jour en cours.</td>       </tr>         </table>  	<p>  	<dt>	<a name=FASTASPLITTER><i>fastasplitter</i> (1) 	<dd>	Split a fasta file into a set of smaller ones   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>fastasplitter</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/fastasplitter.html">fastasplitter</a></td></tr>    	</table>  	<p>  	<dt>	<a name=FASTDNAML><i>FASTDNAML</i> (1.2.2) 	<dd>	Phylognie par la mthode de maximum de vraisemblance (DNAML de Felsenstein).   Voir aussi : <a href="gensoft-evol.html#PHYLIP">PHYLIP</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>fastDNAml</td>      	<td><A HREF="/docs/man/doc/fastDNAml.1">man fastDNAml</a></td>    	</tr>  	<tr>    	<td>bootstrap</td>    	</tr>  	<tr>    	<td>categories</td>    	</tr>  	<tr>    	<td>clean_checkpoints</td>    	</tr>  	<tr>    	<td>clean_jumbles</td>    	</tr>  	<tr>    	<td>fastDNAml_boot</td>    	</tr>  	<tr>    	<td>fastDNAml_loop</td>    	</tr>  	<tr>    	<td>frequencies</td>    	</tr>  	<tr>    	<td>global</td>    	</tr>  	<tr>    	<td>jumble</td>    	</tr>  	<tr>    	<td>n_categories</td>    	</tr>  	<tr>    	<td>out.PID</td>    	</tr>  	<tr>    	<td>outgroup</td>    	</tr>  	<tr>    	<td>printdata</td>    	</tr>  	<tr>    	<td>quickadd</td>    	</tr>  	<tr>    	<td>restart</td>    	</tr>  	<tr>    	<td>scores</td>    	</tr>  	<tr>    	<td>transition</td>    	</tr>  	<tr>    	<td>treefile</td>    	</tr>  	<tr>    	<td>userlengths</td>    	</tr>  	<tr>    	<td>usertree</td>    	</tr>  	<tr>    	<td>usertrees</td>    	</tr>  	<tr>    	<td>weights</td>    	</tr>  	<tr>    	<td>weights_categories</td>    	</tr>  	<tr>    	<td>min_info</td>    	</tr>  	<tr>    	<td>categories_file</td>    	</tr>  	<tr>    	<td>trees2NEXUS</td>    	</tr>  	<tr>    	<td>trees2prolog</td>    	</tr>  	<tr>    	<td>n_files</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td><A HREF="/docs/man/doc/fastDNAml_scripts.1">man fastDNAml_scripts</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/fastdnaml-simple.html">FASTDNAML</a></td></tr>    	</table>  	<p>  	<dt>	<a name=FASTLINK><i>FASTLINK</i> (4.1P) 	<dd>	Analyse de linkage, version rapide.   Voir aussi : <a href="gensoft-genet.html#LINKAGE">LINKAGE</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>lodscore</td>      	<td><A HREF="/docs/man/doc/lodscore.1">man lodscore</a></td>    	</tr>  	<tr>    	<td>ilink</td>      	<td><A HREF="/docs/man/doc/ilink.1">man ilink</a></td>    	</tr>  	<tr>    	<td>linkmap</td>      	<td><A HREF="/docs/man/doc/linkmap.1">man linkmap</a></td>    	</tr>  	<tr>    	<td>mlink</td>    	</tr>  	<tr>    	<td>unknown</td>      	<td><A HREF="/docs/man/doc/unknown.1">man unknown</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://linkage.rockefeller.edu/soft/fastlink/">http://linkage.rockefeller.edu/soft/fastlink/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=FASTRNA><i>FAStRNA</i> (1) 	<dd>	Predicts potential tRNA genes in genomic DNA sequences. FAStRNA-CM relies on a probabilistic model. FAStRNA-CLASS relies on a pattern-matching approach.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>FAStRNA-CM</td>    	</tr>  	<tr>    	<td>FAStRNA-CLASS</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/fastrna.html">FAStRNA</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/FAStRNA/readme.ps">/local/gensoft/doc/FAStRNA/readme.ps</a></td></tr>      	<tr><td><A HREF="http://www-igm.univ-mlv.fr/~mabrouk/">http://www-igm.univ-mlv.fr/~mabrouk/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=FLINQS><i>flinqs</i> (1.1) 	<dd>	Find linker in query sequence   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>flinqs</td>      	<td><A HREF="/docs/man/doc/flinqs.1">man flinqs</a></td>    	</tr>  	</table>  	<p>  	<dt>	<a name=FMTSEQ><i>fmtseq</i>  	<dd>	Conversion de formats de sequence.  Voir aussi : <a href="gensoft-prog.html#SEQIO">SEQIO</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>fmtseq</td>      	<td><A HREF="/docs/man/doc/fmtseq.1">man fmtseq</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/formats-fr.html">fmtseq</a></td></tr>    	</table>  	<p>  	<dt>	<a name=FROMMASE><i>fromMase</i> (1) 	<dd>	Conversion d'un alignement en format Mase vers MSF, clustalw ou fasta.  Le format Mase est pratique pour les logiciels SEAVIEW et phylo_win.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>fromMase</td>    	</tr>  	</table>  	<p>  	<dt>	<a name=FTDOCK><i>ftdock</i> (1.0) 	<dd>	FTDOCK attempts to dock two macromolecules using a fast Fourier transform   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>ftdock</td>      	<td>ftdock</td>    	</tr>  	<tr>    	<td>filtr</td>    	</tr>  	<tr>    	<td>predock.pl</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/ftdock/ftdock-manual.ps">/local/gensoft/doc/ftdock/ftdock-manual.ps</a></td></tr>    	</table>  	<p>  	<dt>	<a name=GARNIER><i>GARNIER</i>  	<dd>	Recherche de structure secondaire d'une protine par la mthode Garnier.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>garnier</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/fasta/fasta20.doc">/local/gensoft/doc/fasta/fasta20.doc</a></td></tr>    	</table>  	<p>  	<dt>	<a name=GAS><i>GAS</i> (2.0) 	<dd>	Analyses gntiques (Genetic Analysis System).   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>gas</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/gas/gman20a.ps">/local/gensoft/doc/gas/gman20a.ps</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/gas/gman20g.ps">/local/gensoft/doc/gas/gman20g.ps</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/gas/examples//">/local/gensoft/doc/gas/examples/</a></td></tr>      	<tr><td><A HREF="http://users.ox.ac.uk/~ayoung/gas.html">http://users.ox.ac.uk/~ayoung/gas.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=GB2XML><i>gb2xml</i> (1.06) 	<dd>	Genbank to XML conversion tool.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>gb2xml</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/gb2xml-simple.html">gb2xml</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="ftp://ftp.pasteur.fr/pub/GenSoft/unix/db_soft/gb2xml">ftp://ftp.pasteur.fr/pub/GenSoft/unix/db_soft/gb2xml</a></td></tr>    	</table>  	<p>  	<dt>	<a name=GCG><i>GCG</i> (10.2) 	<dd>	Environnement GCG pour les programmes d'analyse de squences.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>gcg</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/gcgmanual.html">http://bioweb.pasteur.fr/docs/gcg/gcgmanual.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>Tous les programmes dont le nom commence par GCG, doivent tre utiliss en environnement GCG. Pour y entrer: utiliser la commande gcg une seule fois, l'ordinateur l'indique en commenant ses lignes par gcg: >. Pour en sortir: utiliser la commande exit </td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGBACKTRANSLATE><i>GCG BackTranslate</i>  	<dd>	BackTranslate backtranslates an amino acid sequence into a nucleotide sequence. The output helps you recognize minimally ambiguous regions that might be good for constructing synthetic probes.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>backtranslate</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp backtranslate</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/backtranslate.html">http://bioweb.pasteur.fr/docs/gcg/backtranslate.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGBESTFIT><i>GCG BestFit</i>  	<dd>	BestFit makes an optimal alignment of the best segment of  similarity between two sequences. Optimal alignments are  found by inserting gaps to maximize the number of matches  using the local homology algorithm of Smith and Waterman.     	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>bestfit</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp bestfit</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/bestfit.html">http://bioweb.pasteur.fr/docs/gcg/bestfit.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGBLAST><i>GCG Blast</i>  	<dd>	BLAST searches for sequences similar to a query sequence. The query and the database     searched can be either peptide or nucleic acid in any combination. BLAST can search     databases on your local computer.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>blast</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp blast</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/blast.html">http://bioweb.pasteur.fr/docs/gcg/blast.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGCHOPUP><i>GCG ChopUp</i>  	<dd>	ChopUp  converts a non-GCG sequence file containing lines as  long as 32,000 characters into  a new file containing lines no longer than 50 characters.   The new  file  can be  read  by  Reformat  to create  a GCG-format sequence file.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>chopup</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp chopup</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/chopup.html">http://bioweb.pasteur.fr/docs/gcg/chopup.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGCODONFREQUENCY><i>GCG CodonFrequency</i>  	<dd>	CodonFrequency tabulates codon usage from sequences and/or  existing codon usage tables. The output file is correctly  formatted for input to the CodonPreference, Correspond, and Frames programs.    Voir aussi : <a href="gensoft-na.html#GCGCODONPREFERENCE">GCG CodonPreference</a>, <a href="gensoft-na.html#GCGCORRESPOND">GCG Correspond</a>, <a href="gensoft-na.html#GCGFRAMES">GCG Frames</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>codonfrequency</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp codonfrequency</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/codonfrequency.html">http://bioweb.pasteur.fr/docs/gcg/codonfrequency.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGCODONPREFERENCE><i>GCG CodonPreference</i>  	<dd>	CodonPreference is a frame-specific gene finder that tries  to recognize protein coding sequences by virtue of the  similarity of their codon usage to a codon frequency table or by the bias of their composition (usually GC) in the third position of each codon.    Voir aussi : <a href="gensoft-na.html#GCGCODONFREQUENCY">GCG CodonFrequency</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>codonpreference</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp codonpreference</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/codonpreference.html">http://bioweb.pasteur.fr/docs/gcg/codonpreference.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable </td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGCOILSCAN><i>GCG CoilScan</i>  	<dd>	CoilScan locates coiled-coil segments in protein sequences.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>coilscan</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp coilscan</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/coilscan.html">http://bioweb.pasteur.fr/docs/gcg/coilscan.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGCOMPARE><i>GCG Compare</i>  	<dd>	Compare compares two protein or nucleic acid sequences and  creates a file of the points of similarity between them for plotting with DotPlot. Compare finds the points using either a window/stringency or a word match criterion. The word comparison is 1,000 times faster than the window/stringency comparison, but somewhat less sensitive.   Voir aussi : <a href="gensoft-algt.html#GCGDOTPLOT">GCG DotPlot</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>compare</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp compare</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/compare.html">http://bioweb.pasteur.fr/docs/gcg/compare.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGCOMPOSITION><i>GCG Composition</i>  	<dd>	Composition determines the composition of sequence(s). For  nucleotide sequence(s), Composition also determines dinucleotide and trinucleotide content.     	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>composition</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp composition</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/composition.html">http://bioweb.pasteur.fr/docs/gcg/composition.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGCOMPTABLE><i>GCG CompTable</i>  	<dd>	CompTable creates a scoring matrix using equivalences defined in a simplification scheme such as the one used for Simplify. (See the Chapter 4, Using Data Files in the User's Guide for more information.)   Voir aussi : <a href="gensoft-misc.html#GCGSIMPLIFY">GCG Simplify</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>comptable</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp comptable</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/comptable.html">http://bioweb.pasteur.fr/docs/gcg/comptable.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGCONSENSUS><i>GCG Consensus</i>  	<dd>	Consensus calculates a consensus sequence for a set of  pre-aligned short nucleic acid sequences by tabulating the percent of G, A, T, and C for each position in the set. FitConsensus uses the Consensus output table as a probe to search for the best examples of the derived consensus in other nucleotide sequences.      	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>consensus</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp consensus</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/consensus.html">http://bioweb.pasteur.fr/docs/gcg/consensus.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGCORRESPOND><i>GCG Correspond</i>  	<dd>	Correspond looks for similar patterns of codon usage by  comparing codon frequency tables.    Voir aussi : <a href="gensoft-na.html#GCGCODONFREQUENCY">GCG CodonFrequency</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>correspond</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp correspond</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/correspond.html">http://bioweb.pasteur.fr/docs/gcg/correspond.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGDISTANCES><i>GCG Distances</i>  	<dd>	Distances creates a table of the pairwise distances within  a group of aligned sequences.     	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>distances</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp distances</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/distances.html">http://bioweb.pasteur.fr/docs/gcg/distances.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGDIVERGE><i>GCG Diverge</i>  	<dd>	Diverge estimates the pairwise number of synonymous and  nonsynonymous substitutions per site between two or more aligned nucleic acid sequences that code for proteins. It uses a variant of the method published by Li  et al.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>diverge</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp diverge</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/diverge.html">http://bioweb.pasteur.fr/docs/gcg/diverge.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGDOTPLOT><i>GCG DotPlot</i>  	<dd>	DotPlot makes  a dot-plot with the output file from Compare, FoldRNA, or StemLoop.  Voir aussi : <a href="gensoft-algt.html#GCGCOMPARE">GCG Compare</a>, <a href="gensoft-na.html#GCGSTEMLOOP">GCG StemLoop</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>dotplot</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp dotplot</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/dotplot.html">http://bioweb.pasteur.fr/docs/gcg/dotplot.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGFASTA><i>GCG FastA</i>  	<dd>	FastA does a Pearson and Lipman search for similarity between a query sequence and a group of sequences of  the  same type (nucleic acid or protein).  For nucleotide searches, FastA may be more  sensitive than BLAST.  Voir aussi : <a href="gensoft-algt.html#FASTA">FASTA</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>fasta</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp fasta</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/fasta.html">http://bioweb.pasteur.fr/docs/gcg/fasta.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGFETCH><i>GCG Fetch</i>  	<dd>	Fetch copies GCG sequences or data files from the GCG database into your directory or displays them on your terminal screen.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>fetch</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp fetch</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/fetch.html">http://bioweb.pasteur.fr/docs/gcg/fetch.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGFINDPATTERNS><i>GCG FindPatterns</i>  	<dd>	FindPatterns identifies sequences that contain short  patterns like GAATTC or YRYRYRYR. You can define the  patterns ambiguously and allow mismatches. You can provide the patterns in a file or simply type them in from the terminal.      	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>findpatterns</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp findpatterns</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/findpatterns.html">http://bioweb.pasteur.fr/docs/gcg/findpatterns.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable </td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGFINGERPRINT><i>GCG Fingerprint</i>  	<dd>	Fingerprint identifies the products of T1 ribonuclease digestion.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>fingerprint</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp fingerprint</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/fingerprint.html">http://bioweb.pasteur.fr/docs/gcg/fingerprint.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGFITCONSENSUS><i>GCG FitConsensus</i>  	<dd>	FitConsensus uses a consensus table written by Consensus as  a probe to find the best examples of the consensus in a DNA sequence. You can specify the number of fits you  want to see, and FitConsensus tabulates them with their position, frame, and a statistical measure of their  quality.   Voir aussi : <a href="gensoft-na.html#GCGCONSENSUS">GCG Consensus</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>fitconsensus</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp fitconsensus</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/fitconsensus.html">http://bioweb.pasteur.fr/docs/gcg/fitconsensus.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGFRAMEALIGN><i>GCG FrameAlign</i>  	<dd>	FrameAlign creates an optimal alignment of the best  segment of similarity (local alignment) between a protein sequence and the codons in all possible reading frames of a nucleotide sequence. Optimal alignments may include reading frame shifts.      	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>framealign</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp framealign</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/framealign.html">http://bioweb.pasteur.fr/docs/gcg/framealign.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGFRAMES><i>GCG Frames</i>  	<dd>	Frames shows open reading frames for the six translation  frames of a DNA sequence. Frames can superimpose the pattern of rare codon choices if you provide it with a  codon frequency table.    Voir aussi : <a href="gensoft-na.html#GCGCODONFREQUENCY">GCG CodonFrequency</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>frames</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp frames</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/frames.html">http://bioweb.pasteur.fr/docs/gcg/frames.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable </td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGFRAMESEARCH><i>GCG FrameSearch</i>  	<dd>	FrameSearch searches a group of protein sequences for similarity to one or more nucleotide query sequences, or searches a group of nucleotide sequences for similarity to one or more protein query sequences.  For each sequence comparison, the program finds an optimal alignment between the protein sequence and all possible codons on each strand of the nucleotide sequence.  Optimal alignments may include reading frame shifts.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>framesearch</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp framesearch</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/framesearch.html">http://bioweb.pasteur.fr/docs/gcg/framesearch.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGGAP><i>GCG Gap</i>  	<dd>	Gap uses the algorithm of Needleman and Wunsch to find the  alignment of two complete sequences that maximizes the  number of matches and minimizes the number of gaps.     	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>gap</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp gap</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/gap.html">http://bioweb.pasteur.fr/docs/gcg/gap.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGGAPSHOW><i>GCG GapShow</i>  	<dd>	GapShow displays an alignment by making a graph that shows  the distribution of similarities and gaps. The two input sequences should be aligned with either Gap or  BestFit before they are given to GapShow for display.  Voir aussi : <a href="gensoft-algt.html#GCGGAP">GCG Gap</a>, <a href="gensoft-algt.html#GCGBESTFIT">GCG BestFit</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>gapshow</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp gapshow</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/gapshow.html">http://bioweb.pasteur.fr/docs/gcg/gapshow.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGGROWTREE><i>GCG GrowTree</i>  	<dd>	GrowTree creates a phylogenetic tree from a distance matrix  created by Distances using either the UPGMA or  neighbor-joining method. You can create a text or graphics  output file.    Voir aussi : <a href="gensoft-evol.html#GCGDISTANCES">GCG Distances</a>, <a href="gensoft-evol.html#PHYLIP">PHYLIP</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>growtree</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp growtree</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/growtree.html">http://bioweb.pasteur.fr/docs/gcg/growtree.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable </td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGHELICALWHEEL><i>GCG HelicalWheel</i>  	<dd>	HelicalWheel plots a peptide  sequence as a helical wheel to help you  recognize amphiphilic regions.   Voir aussi : <a href="gensoft-aa.html#GCGPEPPLOT">GCG PepPlot</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>helicalwheel</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp helicalwheel</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/helicalwheel.html">http://bioweb.pasteur.fr/docs/gcg/helicalwheel.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGHTHSCAN><i>GCG HTHScan</i>  	<dd>	HTHScan scans  protein sequences for the presence of helix-turn-helix motifs,  indicative of sequence-specific DNA-binding structures often associated with gene regulation.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>hthscan</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp hthscan</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/hthscan.html">http://bioweb.pasteur.fr/docs/gcg/hthscan.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGISOELECTRIC><i>GCG Isoelectric</i>  	<dd>	Isoelectric plots  the charge as a  function  of pH  for any  peptide sequence.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>isoelectric</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp isoelectric</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/isoelectric.html">http://bioweb.pasteur.fr/docs/gcg/isoelectric.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGMAP><i>GCG Map</i>  	<dd>	Map maps a DNA sequence and displays both strands of the mapped sequence with restriction enzyme cut points above the sequence and protein translations below. Map can also create a peptide map of an amino acid sequence.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>map</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp map</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/map.html">http://bioweb.pasteur.fr/docs/gcg/map.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGMAPPLOT><i>GCG MapPlot</i>  	<dd>	MapPlot displays restriction sites graphically.  If you don't have  a plotter, MapPlot can write a text file that approximates the graph.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>mapplot</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp mapplot</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/mapplot.html">http://bioweb.pasteur.fr/docs/gcg/mapplot.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGMAPSORT><i>GCG MapSort</i>  	<dd>	MapSort finds the coordinates of the restriction enzyme cuts in a DNA sequence  and  sorts the fragments of  the resulting  digest by size. MapSort  can  sort  the  fragments  from single  or  multiple  enzyme digests.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>mapsort</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp mapsort</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/mapsort.html">http://bioweb.pasteur.fr/docs/gcg/mapsort.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGMFOLD><i>GCG MFold</i>  	<dd>	MFold predicts optimal and suboptimal secondary structures for an RNA molecule using the most recent energy minimization method of Zuker.   Voir aussi : <a href="gensoft-na.html#GCGPLOTFOLD">GCG PlotFold</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>mfold</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp mfold</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/mfold.html">http://bioweb.pasteur.fr/docs/gcg/mfold.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGMOMENT><i>GCG Moment</i>  	<dd>	Moment makes a contour plot  of the helical hydrophobic moment of a peptide sequence.   Voir aussi : <a href="gensoft-aa.html#GCGPEPPLOT">GCG PepPlot</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>moment</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp moment</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/moment.html">http://bioweb.pasteur.fr/docs/gcg/moment.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGMOTIFS><i>GCG Motifs</i>  	<dd>	Motifs looks for sequence motifs by searching through  proteins for the patterns defined in the PROSITE Dictionary of Protein Sites and Patterns. Motifs can  display an abstract of the current literature on each of  the motifs it finds.    Voir aussi : <a href="gensoft-aa.html#PROSEARCH">PROSEARCH</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>motifs</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp motifs</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/motifs.html">http://bioweb.pasteur.fr/docs/gcg/motifs.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable </td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGNOOVERLAP><i>GCG NoOverlap</i>  	<dd>	NoOverlap identifies the places where a group of nucleotide  sequences do not share any common subsequences.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>nooverlap</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp nooverlap</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/nooverlap.html">http://bioweb.pasteur.fr/docs/gcg/nooverlap.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable </td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGOLDDISTANCES><i>GCG OldDistances</i>  	<dd>	OldDistances makes a table of the pairwise similarities  within a group of aligned sequences.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>olddistances</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp olddistances</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/olddistances.html">http://bioweb.pasteur.fr/docs/gcg/olddistances.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable </td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGOVERLAP><i>GCG Overlap</i>  	<dd>	Overlap compares two sets of DNA sequences to each other  in both orientations using a WordSearch style comparison.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>overlap</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp overlap</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/overlap.html">http://bioweb.pasteur.fr/docs/gcg/overlap.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable </td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGPAUP><i>GCG PAUP</i>  	<dd>	PAUP (Phylogenetic Analysis Using Parsimony) version in the GCG package. PAUPSearch provides a GCG interface to the         tree-searching options in PAUP (Phylogenetic Analysis Using Parsimony). PAUPDisplay provides a GCG interface to tree         manipulation, diagnosis, and display options in PAUP.   Voir aussi : <a href="gensoft-evol.html#PAUP">PAUP</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>PAUPSearch</td>    	</tr>  	<tr>    	<td>PAUPDisplay</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/paupsearch.html">http://bioweb.pasteur.fr/docs/gcg/paupsearch.html</a></td></tr>      	<tr><td><A HREF="/docs/gcg/paupdisplay.html">http://bioweb.pasteur.fr/docs/gcg/paupdisplay.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>Lancer GCG au pralable. </td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGPEPDATA><i>GCG PepData</i>  	<dd>	PepData translates DNA sequence(s) in all six frames.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>pepdata</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp pepdata</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/pepdata.html">http://bioweb.pasteur.fr/docs/gcg/pepdata.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGPEPPLOT><i>GCG PepPlot</i>  	<dd>	PepPlot   plots   measures   of   protein   secondary  structure  and hydrophobicity in parallel panels of the same plot.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>pepplot</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp pepplot</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/pepplot.html">http://bioweb.pasteur.fr/docs/gcg/pepplot.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGPEPTIDEMAP><i>GCG PeptideMap</i>  	<dd>	PeptideMap creates a peptide map of an amino acid sequence.  Voir aussi : <a href="gensoft-aa.html#GCGPEPTIDESORT">GCG PeptideSort</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>peptidemap</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp peptidemap</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/peptidemap.html">http://bioweb.pasteur.fr/docs/gcg/peptidemap.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGPEPTIDESORT><i>GCG PeptideSort</i>  	<dd>	PeptideSort shows  the peptide  fragments  from  a digest of an amino acid  sequence.  It sorts  the peptides by weight, position, and HPLC retention  at pH 2.1, and shows the composition of each  peptide.  It also prints a summary of the composition of the whole protein.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>peptidesort</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp peptidesort</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/peptidesort.html">http://bioweb.pasteur.fr/docs/gcg/peptidesort.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGPEPTIDESTRUCTURE><i>GCG PeptideStructure</i>  	<dd>	PeptideStructure makes secondary structure  predictions for a peptide sequence.  The predictions include (in addition to alpha, beta, coil, and turn) measures for antigenicity, flexibility, hydrophobicity, and surface   probability.    PlotStructure  displays   the   predictions graphically.   Voir aussi : <a href="gensoft-aa.html#GCGPLOTSTRUCTURE">GCG PlotStructure</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>peptidestructure</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp peptidestructure</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/peptidestructure.html">http://bioweb.pasteur.fr/docs/gcg/peptidestructure.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGPILEUP><i>GCG PileUp</i>  	<dd>	PileUp creates a multiple sequence alignment from a group  of related sequences using progressive, pairwise alignments. It can also plot a tree showing the clustering  relationships used to create the alignment.    Voir aussi : <a href="#CLUSTALW">clustalw</a>, <a href="gensoft-algt.html#GCGPRETTY">GCG Pretty</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>pileup</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp pileup</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/pileup.html">http://bioweb.pasteur.fr/docs/gcg/pileup.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGPLASMIDMAP><i>GCG PlasmidMap</i>  	<dd>	PlasmidMap  draws a circular plot  of a  plasmid construct.   It  can display  restriction patterns, inserts,  and known  genetic elements. The plot is suitable  for publication, record  keeping, or  analysis. It is drawn  from one or more labeling files such as those written by MapSort.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>plasmidmap</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp plasmidmap</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/plasmidmap.html">http://bioweb.pasteur.fr/docs/gcg/plasmidmap.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGPLOTFOLD><i>GCG PlotFold</i>  	<dd>	PlotFold displays the optimal and suboptimal secondary structures for an RNA molecule predicted by MFold.   Voir aussi : <a href="gensoft-na.html#GCGMFOLD">GCG MFold</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>plotfold</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp plotfold</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/plotfold.html">http://bioweb.pasteur.fr/docs/gcg/plotfold.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGPLOTSIMILARITY><i>GCG PlotSimilarity</i>  	<dd>	PlotSimilarity plots the running average of the similarity  among the sequences in a multiple sequence alignment.     	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>plotsimilarity</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp plotsimilarity</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/plotsimilarity.html">http://bioweb.pasteur.fr/docs/gcg/plotsimilarity.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGPLOTSTRUCTURE><i>GCG PlotStructure</i>  	<dd>	PlotStructure plots  the  measures of protein secondary structure  in the output file from PeptideStructure.  The measures can  be shown on parallel  panels of  a  graph  or with  a  two-dimensional "squiggly" representation.   Voir aussi : <a href="gensoft-aa.html#GCGPEPTIDESTRUCTURE">GCG PeptideStructure</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>plotstructure</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp plotstructure</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/plotstructure.html">http://bioweb.pasteur.fr/docs/gcg/plotstructure.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGPRETTY><i>GCG Pretty</i>  	<dd>	Pretty displays multiple sequence alignments and calculates  a consensus sequence. It does not create the alignment; it simply displays it.   Voir aussi : <a href="gensoft-algt.html#GCGPILEUP">GCG PileUp</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>pretty</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp pretty</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/pretty.html">http://bioweb.pasteur.fr/docs/gcg/pretty.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGPRIME><i>GCG Prime</i>  	<dd>	Prime selects  oligonucleotide primers for  a  template DNA sequence. The primers may be  useful for the polymerase chain reaction (PCR) or for DNA sequencing.  You can allow Prime to choose  primers from  the whole template or  limit the  choices to  a particular set of primers  listed in a file.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>prime</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp prime</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/prime.html">http://bioweb.pasteur.fr/docs/gcg/prime.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGPROFILEGAP><i>GCG ProfileGap</i>  	<dd>	ProfileGap makes an optimal alignment between a profile  and one or more sequences.   Voir aussi : <a href="gensoft-algt.html#GCGPROFILEMAKE">GCG ProfileMake</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>profilegap</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp profilegap</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/profilegap.html">http://bioweb.pasteur.fr/docs/gcg/profilegap.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGPROFILEMAKE><i>GCG ProfileMake</i>  	<dd>	ProfileMake creates a position-specific scoring table,  called a profile, that quantitatively represents the information from a group of aligned sequences. The profile can then be used for database searching (ProfileSearch) or sequence alignment (ProfileGap).   Voir aussi : <a href="gensoft-algt.html#GCGPROFILESEARCH">GCG ProfileSearch</a>, <a href="gensoft-algt.html#GCGPROFILEGAP">GCG ProfileGap</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>profilemake</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp profilemake</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/profileanalysis.html">http://bioweb.pasteur.fr/docs/gcg/profileanalysis.html</a></td></tr>      	<tr><td><A HREF="/docs/gcg/profileanalysis.html">http://bioweb.pasteur.fr/docs/gcg/profileanalysis.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGPROFILESCAN><i>GCG ProfileScan</i>  	<dd>	ProfileScan  uses  a  database  of  profiles to  find structural  and sequence motifs in protein sequences.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>profilescan</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp profilescan</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/profilescan.html">http://bioweb.pasteur.fr/docs/gcg/profilescan.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGPROFILESEARCH><i>GCG ProfileSearch</i>  	<dd>	ProfileSearch  uses  a  profile  (representing  a  group  of  aligned sequences) as  a query to search  the database for new sequences with similarity to the  group.  The  profile  is created with  the program ProfileMake.   Voir aussi : <a href="gensoft-algt.html#GCGPROFILEMAKE">GCG ProfileMake</a>, <a href="gensoft-algt.html#GCGPROFILESEGMENTS">GCG ProfileSegments</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>profilesearch</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp profilesearch</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/profilesearch.html">http://bioweb.pasteur.fr/docs/gcg/profilesearch.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGPROFILESEGMENTS><i>GCG ProfileSegments</i>  	<dd>	ProfileSegments  makes optimal  alignments  showing  the segments  of similarity found by ProfileSearch.   Voir aussi : <a href="gensoft-algt.html#GCGPROFILESEARCH">GCG ProfileSearch</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>profilesegments</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp profilesegments</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/profilesegments.html">http://bioweb.pasteur.fr/docs/gcg/profilesegments.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGREFORMAT><i>GCG Reformat</i>  	<dd>	Reformat rewrites sequence file(s), scoring matrix file(s), or enzyme      data file(s) so that they can be read by GCG programs.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>reformat</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp reformat</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/reformat.html">http://bioweb.pasteur.fr/docs/gcg/reformat.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGREPEAT><i>GCG Repeat</i>  	<dd>	Repeat finds direct repeats in sequences. You must set the  size, stringency, and range within which the repeat must occur; all the repeats of that size or greater are  displayed as short alignments.     	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>repeat</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp repeat</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/repeat.html">http://bioweb.pasteur.fr/docs/gcg/repeat.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable </td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGREVERSE><i>GCG Reverse</i>  	<dd>	Reverse reverses and/or complements a sequence.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>reverse</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp reverse</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/reverse.html">http://bioweb.pasteur.fr/docs/gcg/reverse.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGSEG><i>GCG Seg</i>  	<dd>	Seg replaces low complexity regions in protein sequences  with X characters. If a resulting protein sequence is used as a query for a BLAST search, the regions with X  characters are ignored.     Voir aussi : <a href="gensoft-algt.html#GCGBLAST">GCG Blast</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>seg</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp seg</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/seg.html">http://bioweb.pasteur.fr/docs/gcg/seg.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGSHUFFLE><i>GCG Shuffle</i>  	<dd>	Shuffle randomizes the order of the symbols in a sequence without changing the composition.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>shuffle</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp shuffle</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/shuffle.html">http://bioweb.pasteur.fr/docs/gcg/shuffle.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGSIMPLIFY><i>GCG Simplify</i>  	<dd>	Simplify lets you reduce the number of symbols in a sequence. Such a simplification would allow you, for instance, to treat all  hydrophobic amino acids as equivalent.   Voir aussi : <a href="gensoft-misc.html#GCGCOMPTABLE">GCG CompTable</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>simplify</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp simplify</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/simplify.html">http://bioweb.pasteur.fr/docs/gcg/simplify.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGSPSCAN><i>GCG SPScan</i>  	<dd>	SPScan scans  protein sequences  for the presence of secretory signal peptides (SPs).   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>spscan</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp spscan</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/spscan.html">http://bioweb.pasteur.fr/docs/gcg/spscan.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGSTATPLOT><i>GCG StatPlot</i>  	<dd>	StatPlot plots a set of parallel curves from a table of  numbers like the table written by the Window program. The statistics in each column of the table are associated  with a position in the analyzed sequence.     	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>statPlot</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp statPlot</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/statplot.html">http://bioweb.pasteur.fr/docs/gcg/statplot.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGSTEMLOOP><i>GCG StemLoop</i>  	<dd>	StemLoop  finds  stems  (inverted repeats)  within  a  sequence.  You specify the minimum stem length,  minimum and maximum loop sizes, and the  minimum number of  bonds  per stem.  All loops or only  the best loops can be displayed on your screen or written into a file.  Voir aussi : <a href="gensoft-algt.html#GCGDOTPLOT">GCG DotPlot</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>stemloop</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp stemloop</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/stemloop.html">http://bioweb.pasteur.fr/docs/gcg/stemloop.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGSTRINGSEARCH><i>GCG StringSearch</i>  	<dd>	StringSearch identifies sequences by searching for character patterns such as "globin" or     "human" in the sequence documentation.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>stringsearch</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp stringsearch</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/stringsearch.html">http://bioweb.pasteur.fr/docs/gcg/stringsearch.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGTERMINATOR><i>GCG Terminator</i>  	<dd>	Terminator searches for prokaryotic factor-independent RNA polymerase terminators according to the     method of Brendel and Trifonov.     	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>terminator</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp terminator</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/terminator.html">http://bioweb.pasteur.fr/docs/gcg/terminator.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable </td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGTESTCODE><i>GCG TestCode</i>  	<dd>	TestCode helps you identify protein coding sequences by  plotting a measure of the non-randomness of the composition at every third base. The statistic does not  require a codon frequency table.     	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>testcode</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp testcode</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/testcode.html">http://bioweb.pasteur.fr/docs/gcg/testcode.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable </td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGTFASTA><i>GCG TFastA</i>  	<dd>	TFastA does a Pearson  and  Lipman  search  for similarity between  a query peptide sequence and any group of nucleotide sequences.  TFastA translates the nucleotide  sequences in all six reading frames before performing  the comparison.  It  is designed to answer  the question, "What implied peptide sequences in a nucleotide sequence database are similar to my peptide sequence?"    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>tfasta</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp tfasta</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/tfasta.html">http://bioweb.pasteur.fr/docs/gcg/tfasta.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable </td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGTRANSLATE><i>GCG Translate</i>  	<dd>	Translate translates nucleotide sequences into peptide sequences.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>translate</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp translate</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/translate.html">http://bioweb.pasteur.fr/docs/gcg/translate.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGWINDOW><i>GCG Window</i>  	<dd>	Window makes a table of the frequencies of different  sequence patterns within a window as it is moved along a sequence. A pattern is any short sequence like GC or R or  ATG. You can plot the output with the program StatPlot.  Voir aussi : <a href="gensoft-na.html#GCGSTATPLOT">GCG StatPlot</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>window</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp window</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/window.html">http://bioweb.pasteur.fr/docs/gcg/window.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GCGXNU><i>GCG Xnu</i>  	<dd>	Xnu replaces statistically significant tandem repeats in protein sequences with X characters. If a resulting protein sequence is used as a query for a BLAST search, the regions with X characters are ignored.  Voir aussi : <a href="gensoft-algt.html#GCGBLAST">GCG Blast</a>, <a href="gensoft-tools.html#XNU">XNU</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>xnu</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>genhelp xnu</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/gcg/xnu.html">http://bioweb.pasteur.fr/docs/gcg/xnu.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>lancer gcg au pralable</td>       </tr>         </table>  	<p>  	<dt>	<a name=GENEHUNTER><i>GENEHUNTER</i> (2.1r2) 	<dd>	Analyses de liaisons.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>gh</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/gh/gh.ps">/local/gensoft/doc/gh/gh.ps</a></td></tr>    	</table>  	<p>  	<dt>	<a name=GENEMARK><i>GeneMark</i> (2.4b) 	<dd>	Locate genes within a DNA sequence.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>gm</td>      	<td><A HREF="/docs/man/man/gm.1.html">man gm</a></td>    	</tr>  	<tr>    	<td>gc</td>      	<td><A HREF="/docs/man/man/gc.1.html">man gc</a></td>    	</tr>  	<tr>    	<td>matinfo</td>      	<td><A HREF="/docs/man/man/matinfo.1.html">man matinfo</a></td>    	</tr>  	<tr>    	<td>viewmat</td>      	<td><A HREF="/docs/man/man/viewmat.1.html">man viewmat</a></td>    	</tr>  	<tr>    	<td>mkmat</td>      	<td><A HREF="/docs/man/man/mkmat.1.html">man mkmat</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/genemark-simple.html">GeneMark</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://opal.biology.gatech.edu/GeneMark/">http://opal.biology.gatech.edu/GeneMark/</a></td></tr>      	<tr><td><A HREF="/docs/genemark/Manual.html">http://bioweb.pasteur.fr/docs/genemark/Manual.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=GENEMARK.HMM><i>GeneMark.hmm</i> (2.2) 	<dd>	GeneMark.hmm: locates genes within a DNA sequence   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>gmhmme</td>      	<td><A HREF="/docs/man/man/gmhmme.1.html">man gmhmme</a></td>    	</tr>  	<tr>    	<td>gmhmmp</td>      	<td><A HREF="/docs/man/man/gmhmmp.1.html">man gmhmmp</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://opal.biology.gatech.edu/GeneMark/">http://opal.biology.gatech.edu/GeneMark/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=GENEPARSER><i>GeneParser</i> (2.03) 	<dd>	Identification de gnes.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>gp.csh</td>      	<td><A HREF="/docs/man/man/gp.csh.1.html">man gp.csh</a></td>    	</tr>  	<tr>    	<td>gp</td>      	<td><A HREF="/docs/man/man/gp.1.html">man gp</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td>/local/gensoft/lib/geneparser/</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>gp.csh rend l'utilisation plus facile. Ce programme est  un stade relativement exprimental.</td>       </tr>         </table>  	<p>  	<dt>	<a name=GENEVIEW><i>GeneView</i> (1.0b) 	<dd>	Interactive Genbank Entry Visualization   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>geneview</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/GeneView/">/local/gensoft/doc/GeneView</a></td></tr>    	</table>  	<p>  	<dt>	<a name=GENOMEINSPECTOR><i>GenomeInspector</i> (1.0) 	<dd>	Analyse de chromosomes (ORF, facteurs de transcription, ... corrlations entre rgions).[X11]   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>GenomeInspector</td>      	<td><A HREF="/docs/man/doc/GenomeInspector.1">man GenomeInspector</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www.gsf.de/biodv/genomeinspector.html">http://www.gsf.de/biodv/genomeinspector.html</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/GenomeInspector//">/local/gensoft/doc/GenomeInspector/</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/GenomeInspector/example_data/">/local/gensoft/doc/GenomeInspector/example_data</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/GenomeInspector/example_ps/">/local/gensoft/doc/GenomeInspector/example_ps</a></td></tr>    	</table>  	<p>  	<dt>	<a name=GENSCAN><i>GENSCAN</i> (1.0) 	<dd>	A general-purpose gene identification program which analyzes genomic DNA sequences from a variety of organisms including human, other vertebrates, invertebrates and plants.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>genscan</td>      	<td><A HREF="/docs/man/doc/genscan.1">man genscan</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/genscan-simple.html">GENSCAN</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://genes.mit.edu/GENSCAN.html">http://genes.mit.edu/GENSCAN.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=GETENTRY><i>GETENTRY</i>  	<dd>	Recherche par courrier lectronique d'une entre dans les banques de  donnes en donnant le locus.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>getentry</td>      	<td><A HREF="/docs/man/man/getentry.1.html">man getentry</a></td>    	</tr>  	</table>  	<p>  	<dt>	<a name=GFF2PS><i>gff2ps</i> (0.94) 	<dd>	Converting gff-formated genomic data-sets to  PostScript.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>gff2ps</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>gff2ps -h</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/gff2ps.html">gff2ps</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/gff2ps/">/local/gensoft/doc/gff2ps</a></td></tr>    	</table>  	<p>  	<dt>	<a name=GIBBS><i>GIBBS</i> (9_95) 	<dd>	Recherche stochastique du meilleur alignement de sites/motifs sur le  critre du maximum de vraisemblance. Recherche des motifs dtects par gibbs sur une banque.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>gibbs</td>      	<td><A HREF="/docs/man/doc/gibbs.1">man gibbs</a></td>    	</tr>  	<tr>    	<td>scan</td>    	</tr>  	<tr>    	<td>purge</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/gibbs-simple.html">GIBBS</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://bayesweb.wadsworth.org/gibbs/gibbs.html">http://bayesweb.wadsworth.org/gibbs/gibbs.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=GLIMMER><i>GLIMMER</i> (2.02) 	<dd>	(Gene Locator and Interpolated Markov Modeler) Finding genes in microbial DNA.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>build-icm</td>      	<td><A HREF="/docs/man/doc/build-icm.1">man build-icm</a></td>    	</tr>  	<tr>    	<td>glimmer-extract</td>      	<td><A HREF="/docs/man/doc/glimmer-extract.1">man glimmer-extract</a></td>    	</tr>  	<tr>    	<td>glimmer</td>      	<td><A HREF="/docs/man/doc/glimmer.1">man glimmer</a></td>    	</tr>  	<tr>    	<td>long-orfs</td>      	<td><A HREF="/docs/man/doc/long-orfs.1">man long-orfs</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/genes/glimmer-fr.html">GLIMMER</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www.cs.jhu.edu/labs/compbio/glimmer.html">http://www.cs.jhu.edu/labs/compbio/glimmer.html</a></td></tr>      	<tr><td><A HREF="http://www.oup.co.uk/nar/Volume_26/Issue_02/html/gkb128_gml.html">http://www.oup.co.uk/nar/Volume_26/Issue_02/html/gkb128_gml.html</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/glimmer/">/local/gensoft/doc/glimmer</a></td></tr>      	<tr><td><A HREF="http://www.tigr.org/softlab/glimmer/glimmer.html">http://www.tigr.org/softlab/glimmer/glimmer.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=GOLDEN><i>golden</i> (1.0) 	<dd>	Fetch databases entries   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>golden</td>      	<td><A HREF="/docs/man/man/golden.1.html">man golden</a></td>    	</tr>  	<tr>    	<td>goldin</td>      	<td><A HREF="/docs/man/man/goldin.1.html">man goldin</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/golden.html">golden</a></td></tr>    	</table>  	<p>  	<dt>	<a name=GRAILCLNT><i>GRAILCLNT</i> (1.3) 	<dd>	Recherche de rgions codantes, modles de gnes, traductions, sites fonctionnels, rptitions (interface ligne de commande).   Voir aussi : <a href="gensoft-na.html#XGRAIL">XGRAIL</a>, <a href="#NETGRAIL">NETGRAIL</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>grailclnt</td>      	<td><A HREF="/docs/man/doc/grailclnt.1">man grailclnt</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/xgrail/grailclnt//">/local/gensoft/doc/xgrail/grailclnt/</a></td></tr>      	<tr><td><A HREF="http://grail.lsd.ornl.gov/manuals/grail1.3-genquest.9605.shtml">http://grail.lsd.ornl.gov/manuals/grail1.3-genquest.9605.shtml</a></td></tr>      	<tr><td><A HREF="http://compbio.ornl.gov/Grail-1.3">http://compbio.ornl.gov/Grail-1.3</a></td></tr>      	<tr><td><A HREF="http://compbio.ornl.gov/grailexp">http://compbio.ornl.gov/grailexp</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>The GRAIL email server has been discontinued.</td>       </tr>         </table>  	<p>  	<dt>	<a name=GRAMM><i>Gramm</i>  	<dd>	Programme de docking entre deux macromolcules.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>  	</tr>  	<tr>  	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td>/usr/local/gensoft/doc/gramm/</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>disponible seulement sur les stations Silicon Graphics du SIS</td>       </tr>         </table>  	<p>  	<dt>	<a name=GRASP><i>Grasp</i>  	<dd>	Analyse et modlisation des proprits de surface.[X11]   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>  	</tr>  	<tr>  	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td>/usr/local/gensoft/packages/Grasp/manual</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>disponible seulement sur les stations Silicon Graphics du SIS</td>       </tr>         </table>  	<p>  	<dt>	<a name=GRS><i>GRS</i> (1.1) 	<dd>	A Graphic Tool for Genome Retrieval and Segment Analysis   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>grs</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www.bioinformatics.org/~thomas/software/grs/">http://www.bioinformatics.org/~thomas/software/grs/</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>Set database choice for blast in Preferences menu.</td>       </tr>         </table>  	<p>  	<dt>	<a name=GRUPPI><i>gruppi</i> (7) 	<dd>	The program gives the list of clusters of binding  sites (at least 2 sites in max 300 bp) whose score is  above the threshold specified in a matrix file.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>gruppi</td>      	<td><A HREF="/docs/man/doc/gruppi.1">man gruppi</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/gruppi-simple.html">gruppi</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/gruppi//">/local/gensoft/doc/gruppi/</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>You can find matrices in /local/gensoft/lib/gruppi/matrices</td>       </tr>         </table>  	<p>  	<dt>	<a name=HMMEDIT><i>HMMEDIT</i> (7) 	<dd>	diteur graphique de modles HMM de format SAM.[X11]   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>hmmedit</td>      	<td>man hmmedit</td>    	</tr>  	</table>  	<p>  	<dt>	<a name=HMMER><i>hmmer</i> (2.2g) 	<dd>	HMMER - profile hidden Markov model software    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>afetch</td>    	</tr>  	<tr>    	<td>alistat</td>    	</tr>  	<tr>    	<td>hmmalign</td>      	<td><A HREF="/docs/man/man/hmmalign.1.html">man hmmalign</a></td>    	</tr>  	<tr>    	<td>hmmbuild</td>      	<td><A HREF="/docs/man/man/hmmbuild.1.html">man hmmbuild</a></td>    	</tr>  	<tr>    	<td>hmmcalibrate</td>      	<td><A HREF="/docs/man/man/hmmcalibrate.1.html">man hmmcalibrate</a></td>    	</tr>  	<tr>    	<td>hmmconvert</td>      	<td><A HREF="/docs/man/man/hmmconvert.1.html">man hmmconvert</a></td>    	</tr>  	<tr>    	<td>hmmemit</td>      	<td><A HREF="/docs/man/man/hmmemit.1.html">man hmmemit</a></td>    	</tr>  	<tr>    	<td>hmmfetch</td>      	<td><A HREF="/docs/man/man/hmmfetch.1.html">man hmmfetch</a></td>    	</tr>  	<tr>    	<td>hmmindex</td>      	<td><A HREF="/docs/man/man/hmmindex.1.html">man hmmindex</a></td>    	</tr>  	<tr>    	<td>hmmpfam</td>      	<td><A HREF="/docs/man/man/hmmpfam.1.html">man hmmpfam</a></td>    	</tr>  	<tr>    	<td>hmmsearch</td>      	<td><A HREF="/docs/man/man/hmmsearch.1.html">man hmmsearch</a></td>    	</tr>  	<tr>    	<td>seqstat</td>    	</tr>  	<tr>    	<td>sfetch</td>    	</tr>  	<tr>    	<td>shuffle</td>    	</tr>  	<tr>    	<td>sindex</td>    	</tr>  	<tr>    	<td>sreformat</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td><A HREF="/docs/man/man/hmmer.1.html">man hmmer</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/motif/hmmer-fr.html">hmmer</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/hmmer/Userguide.pdf">/local/gensoft/doc/hmmer/Userguide.pdf</a></td></tr>      	<tr><td><A HREF="http://hmmer.wustl.edu/">http://hmmer.wustl.edu/</a></td></tr>      	<tr><td><A HREF="http://pfam.wustl.edu/">http://pfam.wustl.edu/</a></td></tr>      	<tr><td><A HREF="http://www.sanger.ac.uk/Pfam/help/">http://www.sanger.ac.uk/Pfam/help/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=HOBACGEN><i>HOBACGEN</i> (1.3) 	<dd>	Bases de donnes et outils pour l'analyse comparative de gnes homologues. [X11]   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>hobacgen</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://pbil.univ-lyon1.fr/databases/hobacgen.html">http://pbil.univ-lyon1.fr/databases/hobacgen.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=HOMOLOGY><i>homology</i> (1.0) 	<dd>	SCMF Homology Modelling Program   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>homology</td>      	<td><A HREF="/docs/man/doc/homology.1">man homology</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/homology.html">homology</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/homology/test/">/local/gensoft/doc/homology/test</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/homology/LISEZMOI">/local/gensoft/doc/homology/LISEZMOI</a></td></tr>    	</table>  	<p>  	<dt>	<a name=HTML4BLAST><i>html4blast</i> (1.6a) 	<dd>	html4blast is a simple hypertext Blast output formatter. It provides links to retrieve databanks entries from their accessions numbers or names, via www servers and a graphical alignment summary.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>html4blast</td>      	<td><A HREF="/docs/man/man/html4blast.1.html">man html4blast</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/html4blast.html">html4blast</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="ftp://ftp.pasteur.fr/pub/GenSoft/unix/alignment/Blast_tools/Html4blast/">ftp://ftp.pasteur.fr/pub/GenSoft/unix/alignment/Blast_tools/Html4blast/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=INCA><i>inca</i> (1) 	<dd>	Iterative Neighborhood Cluster Analysis   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>inca</td>      	<td><A HREF="/docs/man/doc/inca.1">man inca</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://itsa.ucsf.edu/~gram/home/inca/">http://itsa.ucsf.edu/~gram/home/inca/</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/inca/examples//">/local/gensoft/doc/inca/examples/</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>inca /local/gensoft/doc/inca/examples/YRO2_YEAST.1.html </td>       </tr>         </table>  	<p>  	<dt>	<a name=INDENTTREE><i>indenttree</i> (1.0) 	<dd>	Affiche une treefile en format texte, avec une indentation indiquant la structure.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>indenttree</td>    	</tr>  	</table>  	<p>  	<dt>	<a name=JALVIEW><i>jalview</i> (1.7.5b) 	<dd>	Editeur d'alignement.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>jalview</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/jalview/contents.html">http://bioweb.pasteur.fr/docs/jalview/contents.html</a></td></tr>      	<tr><td><A HREF="/docs/jalview/help.html">http://bioweb.pasteur.fr/docs/jalview/help.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>usage: jalview aligfile format</td>       </tr>         </table>  	<p>  	<dt>	<a name=LALNVIEW><i>LALNVIEW</i> (2.1) 	<dd>	Affichage graphique d'un alignement produit par SIM,  LFASTA ou LALIGN. Sites actifs, motifs, domaines...[X11]   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>lalnview</td>      	<td><A HREF="/docs/man/doc/lalnview.1">man lalnview</a></td>    	</tr>  	<tr>    	<td>sim</td>      	<td><A HREF="/docs/man/doc/sim.1">man sim</a></td>    	</tr>  	</table>  	<p>  	<dt>	<a name=LAMARC><i>LAMARC</i> (feb-96) 	<dd>	"FLUCTUATE uses Metropolis-Hastings sampling to estimate Theta (4Ne\mu) and exponential growth rate based on samples of nucleotide squences from a population: it is an extension of our previous program COALESCE (which estimated only Theta and assumed constant population size)."   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>coalesce</td>      	<td><A HREF="/docs/man/doc/coalesce.1">man coalesce</a></td>    	</tr>  	<tr>    	<td>fluctuate</td>      	<td><A HREF="/docs/man/doc/fluctuate.1">man fluctuate</a></td>    	</tr>  	</table>  	<p>  	<dt>	<a name=LASSAP><i>LASSAP</i> (1.2.1b) 	<dd>	(LArge Scale Sequence compArison Package) Logiciel de comparaison de squences. La plupart des algorithmes de comparaison sont proposs.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>lspextend</td>    	</tr>  	<tr>    	<td>lspread</td>    	</tr>  	<tr>    	<td>lspres</td>    	</tr>  	<tr>    	<td>lspvres</td>    	</tr>  	<tr>    	<td>lspcnx</td>    	</tr>  	<tr>    	<td>lspbank</td>    	</tr>  	<tr>    	<td>lspsplit</td>    	</tr>  	<tr>    	<td>lsprebank</td>    	</tr>  	<tr>    	<td>lspcalc</td>    	</tr>  	<tr>    	<td>lspvbank</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>lspextend -h</td></tr>      	<tr><td>lspread -h</td></tr>      	<tr><td>lspres -h</td></tr>      	<tr><td>lspvres -h</td></tr>      	<tr><td>lspcnx -h</td></tr>      	<tr><td>lspbank -h</td></tr>      	<tr><td>lspsplit -h</td></tr>      	<tr><td>lsprebank -h</td></tr>      	<tr><td>lspcalc -h</td></tr>      	<tr><td>lspvbank -h</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/LASSAP/">http://bioweb.pasteur.fr/docs/LASSAP/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=LCP><i>Lcp</i> (1992) 	<dd>	Local Content Program:  a program for identifying regions of a sequence satisfying local content requirements.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>Lcp</td>      	<td><A HREF="/docs/man/doc/Lcp.1">man Lcp</a></td>    	</tr>  	</table>  	<p>  	<dt>	<a name=LINKAGE><i>LINKAGE</i> (5.1) 	<dd>	Analyse de linkage.   Voir aussi : <a href="gensoft-genet.html#FASTLINK">FASTLINK</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>lodscore</td>    	</tr>  	<tr>    	<td>ilink</td>    	</tr>  	<tr>    	<td>linkmap</td>    	</tr>  	<tr>    	<td>mlink</td>    	</tr>  	<tr>    	<td>unknown</td>    	</tr>  	<tr>    	<td>clodscore</td>    	</tr>  	<tr>    	<td>cilink</td>    	</tr>  	<tr>    	<td>cmap</td>    	</tr>  	<tr>    	<td>cfactor</td>    	</tr>  	<tr>    	<td>xlodscore</td>    	</tr>  	<tr>    	<td>xilink</td>    	</tr>  	<tr>    	<td>xmap</td>    	</tr>  	<tr>    	<td>lsp</td>    	</tr>  	<tr>    	<td>lcp</td>    	</tr>  	<tr>    	<td>lrp</td>    	</tr>  	<tr>    	<td>preplink</td>    	</tr>  	<tr>    	<td>makeped</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td><A HREF="/docs/man/doc/linkage.1">man linkage</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/linkage/linkhelp.txt">/local/gensoft/doc/linkage/linkhelp.txt</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/linkage/">/local/gensoft/doc/linkage</a></td></tr>      	<tr><td><A HREF="http://linkage.rockefeller.edu/soft/linkage/">http://linkage.rockefeller.edu/soft/linkage/</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>Pour excuter les versions "linkage" (Lathrop et al) des programmes lodscore, ilink, linkmap, mlink : lancer ces programmes avec l'option "-L", car par defaut,  ce sont les versions FASTLINK qui sont lances.</td>       </tr>         </table>  	<p>  	<dt>	<a name=LOADSEQ><i>loadseq</i>  	<dd>	This utility allows you to concatenate many sequences. Available on the Web only.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>  	</tr>  	<tr>  	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/loadseq-simple.html">loadseq</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/loadseq/howto.html">/local/gensoft/doc/loadseq/howto.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=LOKI><i>loki</i> (2.4.5) 	<dd>	A package for multipoint linkage analysis on large pedigrees using Reversible jump Markov chain Monte Carlo    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>loki</td>      	<td><A HREF="/docs/man/doc/loki.1">man loki</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://loki.homeunix.net/loki_doc/index.html">http://loki.homeunix.net/loki_doc/index.html</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/loki//">/local/gensoft/doc/loki/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=LVB><i>lvb</i> (1.0) 	<dd>	Reconstructing evolution with parsimony and simulated annealing   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>lvb</td>      	<td><A HREF="/docs/man/doc/lvb.1">man lvb</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/lvb.html">lvb</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www.rubic.reading.ac.uk/lvb">http://www.rubic.reading.ac.uk/lvb</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/lvb/test/">/local/gensoft/doc/lvb/test</a></td></tr>    	</table>  	<p>  	<dt>	<a name=MAGPIE><i>MAGPIE</i> (N/A) 	<dd>	Multipurpose Automated Genome Project Investigation Environment.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>  	</tr>  	<tr>  	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www.mcs.anl.gov/home/gaasterl/magpie.html">http://www.mcs.anl.gov/home/gaasterl/magpie.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>Please contact help@pasteur.fr if you are interested.</td>       </tr>         </table>  	<p>  	<dt>	<a name=MALIGN><i>malign</i> (1.99) 	<dd>	    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>malign</td>      	<td><A HREF="/docs/man/doc/malign.1">man malign</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/malign/">/local/gensoft/doc/malign</a></td></tr>    	</table>  	<p>  	<dt>	<a name=MAP><i>MAP</i>  	<dd>	Alignements multiples.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>map</td>      	<td><A HREF="/docs/man/doc/map.1">man map</a></td>    	</tr>  	</table>  	<p>  	<dt>	<a name=MAPMAKER><i>MAPMAKER</i>  	<dd>	Analyses de liaison non paramtriques.  Voir aussi : <a href="gensoft-genet.html#MAPMAKER/QTL">MAPMAKER/QTL</a>, <a href="gensoft-genet.html#MAPMAKER/SIBS">MAPMAKER/SIBS</a>, <a href="gensoft-genet.html#MAPMAKER/HOMOZ">MAPMAKER/HOMOZ</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>mapmaker</td>      	<td><A HREF="/docs/man/doc/mapmaker.1">man mapmaker</a></td>    	</tr>  	<tr>    	<td>xmapmaker</td>    	</tr>  	<tr>    	<td>qtl</td>      	<td><A HREF="/docs/man/doc/qtl.1">man qtl</a></td>    	</tr>  	<tr>    	<td>xqtl</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www.genome.wi.mit.edu/genome_software/other/mapmaker.html">http://www.genome.wi.mit.edu/genome_software/other/mapmaker.html</a></td></tr>      	<tr><td><A HREF="http://www.genome.wi.mit.edu/genome_software/other/mapmaker.ps">http://www.genome.wi.mit.edu/genome_software/other/mapmaker.ps</a></td></tr>    	</table>  	<p>  	<dt>	<a name=MAPMAKER/HOMOZ><i>MAPMAKER/HOMOZ</i>  	<dd>	Analyses de liaison non paramtriques par la recherche d'homozygotie.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>homoz</td>      	<td><A HREF="/docs/man/doc/homoz.1">man homoz</a></td>    	</tr>  	</table>  	<p>  	<dt>	<a name=MAPMAKER/QTL><i>MAPMAKER/QTL</i> (3.0) 	<dd>	Analyse de liaison. Caractres quantitatifs (QTL) ou qualitatif dans des croisements d'animaux consanguins.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>mapmaker</td>      	<td><A HREF="/docs/man/doc/mapmaker.1">man mapmaker</a></td>    	</tr>  	<tr>    	<td>xmapmaker</td>    	</tr>  	<tr>    	<td>qtl</td>      	<td><A HREF="/docs/man/doc/qtl.1">man qtl</a></td>    	</tr>  	<tr>    	<td>xqtl</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www-genome.wi.mit.edu/genome_software/other/qtl.html">http://www-genome.wi.mit.edu/genome_software/other/qtl.html</a></td></tr>      	<tr><td><A HREF="http://www-genome.wi.mit.edu/genome_software/other/qtl.ps">http://www-genome.wi.mit.edu/genome_software/other/qtl.ps</a></td></tr>    	</table>  	<p>  	<dt>	<a name=MAPMAKER/SIBS><i>MAPMAKER/SIBS</i> (2.1) 	<dd>	Analyses de liaison non paramtriques par la mthode  des germains atteints.     	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>sibs</td>      	<td><A HREF="/docs/man/doc/sibs.1">man sibs</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/mapmaker/sibs/">/local/gensoft/doc/mapmaker/sibs</a></td></tr>    	</table>  	<p>  	<dt>	<a name=MASE><i>MASE</i> (3.1) 	<dd>	diteur d'alignement multiple.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>mase</td>      	<td><A HREF="/docs/man/man/mase.1.html">man mase</a></td>    	</tr>  	<tr>    	<td>browser</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/mase/Doc//">/local/gensoft/doc/mase/Doc/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=MATINSPECTOR><i>MatInspector</i> (2.2) 	<dd>	MatInd/MatInspector. MatInspector recherche des sites de liaison dans une squence d'acides  nucliques. Il utilise la description gnre par le programme MatInd.   Voir aussi : <a href="gensoft-na.html#CONSINSPECTOR">ConsInspector</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>matind</td>      	<td><A HREF="/docs/man/doc/matind.1">man matind</a></td>    	</tr>  	<tr>    	<td>matinspector</td>      	<td><A HREF="/docs/man/doc/matinspector.1">man matinspector</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www.gsf.de/biodv/matinspector.html">http://www.gsf.de/biodv/matinspector.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=MCSIM><i>MCSim</i> (4.1) 	<dd>	Programme de simulation Monte-Carlo.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>Mod</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://central.pasteur.fr/mcsim/MCSim.manual.html">http://central.pasteur.fr/mcsim/MCSim.manual.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>Contacter help@pasteur.fr pour l'utilisation.</td>       </tr>         </table>  	<p>  	<dt>	<a name=MEGA2><i>mega2</i> (2.3.4) 	<dd>	Manipulation Environment for Genetic Analyses.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>mega2</td>      	<td><A HREF="/docs/man/doc/mega2.1">man mega2</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/mega2">http://bioweb.pasteur.fr/docs/mega2</a></td></tr>    	</table>  	<p>  	<dt>	<a name=MELTING><i>MELTING</i> (4.2d) 	<dd>	This program computes for an oligonucleotide, the  enthalpie, the entropy and the melting temperature  of the binding to its complementary template.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>melting</td>      	<td><A HREF="/docs/man/doc/melting.1">man melting</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/melting.html">MELTING</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www.pasteur.fr/recherche/unites/neubiomol/meltinghome.html">http://www.pasteur.fr/recherche/unites/neubiomol/meltinghome.html</a></td></tr>      	<tr><td><A HREF="/docs/melting/">http://bioweb.pasteur.fr/docs/melting/</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/MELTING//">/local/gensoft/doc/MELTING/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=MEME><i>MEME</i> (3.0.3) 	<dd>	Multiple EM for Motif Elicitation. Dcouverte de motifs dans un groupe de squences relatives (ADN ou protines). Recherche de ces motifs dans les banques.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>meme</td>      	<td><A HREF="/docs/man/man/meme.1.html">man meme</a></td>    	</tr>  	<tr>    	<td>mast</td>      	<td><A HREF="/docs/man/doc/mast.1">man mast</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/motif/meme/">MEME</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/meme/tests/">/local/gensoft/doc/meme/tests/</a></td></tr>      	<tr><td><A HREF="http://central.pasteur.fr/seqanal/motif/meme/meme-intro.html">http://central.pasteur.fr/seqanal/motif/meme/meme-intro.html</a></td></tr>      	<tr><td><A HREF="http://central.pasteur.fr/seqanal/motif/meme/mast-intro.html">http://central.pasteur.fr/seqanal/motif/meme/mast-intro.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=MERLIN><i>merlin</i> (0.9.8) 	<dd>	MERLIN uses sparse trees to represent gene flow in pedigrees and is one of  the fastest pedigree analysis packages  around (Abecasis et al, 2002).   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>merlin</td>      	<td><A HREF="/docs/man/doc/merlin.1">man merlin</a></td>    	</tr>  	<tr>    	<td>minx</td>    	</tr>  	<tr>    	<td>merlin-regress</td>    	</tr>  	<tr>    	<td>pedstats</td>    	</tr>  	<tr>    	<td>pedwipe</td>    	</tr>  	<tr>    	<td>pedmerge</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www.sph.umich.edu/csg/abecasis/Merlin/index.html">http://www.sph.umich.edu/csg/abecasis/Merlin/index.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=MFOLD><i>MFOLD</i> (2.3) 	<dd>	Prediction of RNA secondary structure by Energy Minimization (Zuker).   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>mfold</td>      	<td><A HREF="/docs/man/doc/mfold.1">man mfold</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/mfold-simple.html">MFOLD</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/mfold/doc/manual.ps">/local/gensoft/doc/mfold/doc/manual.ps</a></td></tr>      	<tr><td><A HREF="http://www.bioinfo.rpi.edu/applications/mfold/">http://www.bioinfo.rpi.edu/applications/mfold/</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>There are a lot of other Unix commands for mfold not listed here for simplicity.</td>       </tr>         </table>  	<p>  	<dt>	<a name=MINORE><i>MINORE</i>  	<dd>	Recherche automatise de similarits dans les banques avec le serveur BLAST du NCBI. Les rsultats  sont filtrs en fonction des scores et envoys par  email.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>minore</td>      	<td><A HREF="/docs/man/doc/minore.1">man minore</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/minore//">/local/gensoft/doc/minore/</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>Voir les fichiers d'exemples.</td>       </tr>         </table>  	<p>  	<dt>	<a name=MINT><i>Mint</i> (3.0) 	<dd>	Une interface graphique simple pour Modeller.[X11]  Voir aussi : <a href="gensoft-graph.html#MODELLER">MODELLER</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>mint</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/Mint/mint.ps">/local/gensoft/doc/Mint/mint.ps</a></td></tr>    	</table>  	<p>  	<dt>	<a name=MMSEARCH><i>mmsearch</i> (1.0) 	<dd>	Find arrangements in motif match databases   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>mmsearch</td>      	<td><A HREF="/docs/man/doc/mmsearch.1">man mmsearch</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/mmsearch/index.html">http://bioweb.pasteur.fr/docs/mmsearch/index.html</a></td></tr>      	<tr><td><A HREF="http://hits.isb-sib.ch/doc/wwwmmsearch.shtml">http://hits.isb-sib.ch/doc/wwwmmsearch.shtml</a></td></tr>    	</table>  	<p>  	<dt>	<a name=MODELLER><i>MODELLER</i> (4) 	<dd>	Modlisation de structure de protines par homologie.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>mod4</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://central.pasteur.fr/docs/modeller/manual.html">http://central.pasteur.fr/docs/modeller/manual.html</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/modeller/manual.ps">/local/gensoft/doc/modeller/manual.ps</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/modeller/examples//">/local/gensoft/doc/modeller/examples/</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>La documentation correspond  la version 3. </td>       </tr>         </table>  	<p>  	<dt>	<a name=MOLMOL><i>MOLMOL</i> (2.2.0) 	<dd>	Manipulations et visualisation de molcules.[X11]   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>molmol</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/molmol/manual.ps">/local/gensoft/doc/molmol/manual.ps</a></td></tr>      	<tr><td><A HREF="http://www.mol.biol.ethz.ch/wuthrich/software/molmol/">http://www.mol.biol.ethz.ch/wuthrich/software/molmol/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=MOLPHY><i>MOLPHY</i> (2.3b3) 	<dd>	Analyses phylogntiques : maximum de vraisemblance et neighbor-joining.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>protml</td>    	</tr>  	<tr>    	<td>nucml</td>    	</tr>  	<tr>    	<td>protst</td>    	</tr>  	<tr>    	<td>nucst</td>    	</tr>  	<tr>    	<td>njdist</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td><A HREF="/docs/man/doc/molphy.1">man molphy</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/prot_nucml.html">MOLPHY</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/molphy/">/local/gensoft/doc/molphy</a></td></tr>    	</table>  	<p>  	<dt>	<a name=MOLSCRIPT><i>MOLSCRIPT</i> (2.1.2) 	<dd>	generer les images a partir d'un fichier  PDB...  X11/OpenGL (il faut un serveur X  qui supporte l'extension XGL)[X11]   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>molscript</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/molscript/">/local/gensoft/doc/molscript</a></td></tr>    	</table>  	<p>  	<dt>	<a name=MORGAN><i>MORGAN</i> (1997) 	<dd>	Finding genes in eukaryotic DNA sequences.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>morgan</td>      	<td><A HREF="/docs/man/doc/morgan.1">man morgan</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/morgan-simple.html">MORGAN</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www.cs.jhu.edu/labs/compbio/morgan.html">http://www.cs.jhu.edu/labs/compbio/morgan.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=MREPS><i>mreps</i> (2.1) 	<dd>	Identification de repetitions contigues dans les sequences nucleiques.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>mreps</td>      	<td><A HREF="/docs/man/doc/mreps.1">man mreps</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/mreps.html">mreps</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/mreps/">/local/gensoft/doc/mreps</a></td></tr>      	<tr><td><A HREF="http://www.loria.fr/~kucherov/software/mreps/">http://www.loria.fr/~kucherov/software/mreps/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=MRTRANS><i>MRTRANS</i> (1992) 	<dd>	Recherche un alignement de cDNA  partir de l'alignement correspondant de protines.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>mrtrans</td>      	<td><A HREF="/docs/man/man/mrtrans.1.html">man mrtrans</a></td>    	</tr>  	</table>  	<p>  	<dt>	<a name=MSA><i>MSA</i> (2.1) 	<dd>	(Multiple Sequence Alignment) Alignements multiples.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>msa</td>      	<td><A HREF="/docs/man/man/msa.1.html">man msa</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/msa/">/local/gensoft/doc/msa</a></td></tr>      	<tr><td><A HREF="http://www.techfak.uni-bielefeld.de/bcd/Lectures/kececioglu.html">http://www.techfak.uni-bielefeld.de/bcd/Lectures/kececioglu.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=MSPCRUNCH><i>MSPcrunch</i> (2.4a) 	<dd>	Traitement des rsultats de BLAST pour BLIXEM (affichage des rsultats sous la forme d'un alignement).  Voir aussi : <a href="gensoft-algt.html#BLIXEM">BLIXEM</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>MSPcrunch</td>      	<td><A HREF="/docs/man/doc/MSPcrunch.1">man MSPcrunch</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/MSPcrunch/MSPcrunch2.ps">/local/gensoft/doc/MSPcrunch/MSPcrunch2.ps</a></td></tr>    	</table>  	<p>  	<dt>	<a name=MUMMER><i>MUMmer</i> (1.0) 	<dd>	(maximal unique matches) A system for aligning whole genome sequences.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>make-align</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td><A HREF="/docs/man/doc/MUMmer.1">man MUMmer</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www.tigr.org/~salzberg/MUMmer.pdf">http://www.tigr.org/~salzberg/MUMmer.pdf</a></td></tr>    	</table>  	<p>  	<dt>	<a name=MVIEW><i>MVIEW</i> (1.47.3) 	<dd>	A tool for converting the results of a sequence database search  into the form of a coloured multiple alignment of hits stacked  against the query.  Alternatively, an existing multiple alignment can be processed.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>mview</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>mview -help</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/mview_alig-simple.html">MVIEW</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/mview/">http://bioweb.pasteur.fr/docs/mview/</a></td></tr>      	<tr><td><A HREF="/seqanal/interfaces/mview_blast-simple.html">http://bioweb.pasteur.fr/seqanal/interfaces/mview_blast-simple.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=NACCESS><i>naccess</i> (2.1.1) 	<dd>	Le calcul du surface accessible d'une molecule.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>naccess</td>      	<td><A HREF="/docs/man/doc/naccess.1">man naccess</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/naccess/README">/local/gensoft/doc/naccess/README</a></td></tr>    	</table>  	<p>  	<dt>	<a name=NAMOT><i>namot</i> (2.1.6) 	<dd>	modelisation d'ADN (Nucleic Acid MOdeling Tool)[X11]   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>namot2</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="http://namot.lanl.gov">namot</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/namot//">/local/gensoft/doc/namot/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=NENTREZ><i>Nentrez</i> (7.50) 	<dd>	Recherches labores dans les banques de squences, dans MEDLINE et dans les banques gnomiques, au NCBI.[X11]   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>Nentrez</td>    	</tr>  	<tr>    	<td>Nentrcmd</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>Nentrcmd -h -p manual</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www3.ncbi.nlm.nih.gov/Entrez/entrezhelp.html">http://www3.ncbi.nlm.nih.gov/Entrez/entrezhelp.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>Nentrez est une version client-serveur graphique. La version ligne de commande est Nentrcmd. Il existe aussi une version Macintosh: <A HREF="ftp://ftp.pasteur.fr/pub/GenSoft/Macintosh/db_soft/">ftp://ftp.pasteur.fr/pub/GenSoft/Macintosh/db_soft/</A></td>       </tr>         </table>  	<p>  	<dt>	<a name=NETGRAIL><i>netgrail</i> (0.03) 	<dd>	A simple perl client used to create valid requests to the  GRAIL server.  Voir aussi : <a href="gensoft-na.html#XGRAIL">XGRAIL</a>, <a href="gensoft-na.html#GRAILCLNT">GRAILCLNT</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>netgrail</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>netgrail -h</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://compbio.ornl.gov/Grail-1.3/help/">http://compbio.ornl.gov/Grail-1.3/help/</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/netgrail//">/local/gensoft/doc/netgrail/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=NJPLOT><i>NJPLOT</i>  	<dd>	diteur graphique d'arbres phylogntiques.[X11]   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>njplot</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://pbil.univ-lyon1.fr/software/njplot.html">http://pbil.univ-lyon1.fr/software/njplot.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>Version Macintosh: <A HREF="ftp://ftp.pasteur.fr/pub/GenSoft/Macintosh/evolution/">ftp://ftp.pasteur.fr/pub/GenSoft/Macintosh/evolution/</A></td>       </tr>         </table>  	<p>  	<dt>	<a name=NNSSP><i>NNSSP</i> (1) 	<dd>	Prediction of protein secondary structure  by combinin nearest-neighbr algorithms and multiple sequence  alignment.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>nnssp</td>      	<td><A HREF="/docs/man/doc/nnssp.1">man nnssp</a></td>    	</tr>  	<tr>    	<td>clu2nnssp</td>      	<td><A HREF="/docs/man/doc/clu2nnssp.1">man clu2nnssp</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/nnssp-simple.html">NNSSP</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>clu2nnssp is written by Nicolas Le Novre (lenov@pasteur.fr)</td>       </tr>         </table>  	<p>  	<dt>	<a name=OC1><i>OC1</i> (3) 	<dd>	Construction d'arbres de dcision.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>mktree</td>      	<td><A HREF="/docs/man/doc/mktree.1">man mktree</a></td>    	</tr>  	<tr>    	<td>gendata</td>      	<td><A HREF="/docs/man/doc/gendata.1">man gendata</a></td>    	</tr>  	<tr>    	<td>oc1-display</td>      	<td><A HREF="/docs/man/doc/oc1-display.1">man oc1-display</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td><A HREF="/docs/man/doc/oc1.1">man oc1</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/oc1/sample_session">/local/gensoft/doc/oc1/sample_session</a></td></tr>      	<tr><td><A HREF="http://www.cs.jhu.edu/~salzberg/announce-oc1.html">http://www.cs.jhu.edu/~salzberg/announce-oc1.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=PAL><i>PAL</i> (0.8) 	<dd>	Phylogenetic Analysis Library (Java)   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>concat</td>    	</tr>  	<tr>    	<td>dropgaps</td>    	</tr>  	<tr>    	<td>dropsites</td>    	</tr>  	<tr>    	<td>dropunknowns</td>    	</tr>  	<tr>    	<td>evolve</td>    	</tr>  	<tr>    	<td>lstree</td>    	</tr>  	<tr>    	<td>mldist</td>    	</tr>  	<tr>    	<td>mltree</td>    	</tr>  	<tr>    	<td>njtree</td>    	</tr>  	<tr>    	<td>reformat</td>    	</tr>  	<tr>    	<td>reroot</td>    	</tr>  	<tr>    	<td>showtree</td>    	</tr>  	<tr>    	<td>splitcodon</td>    	</tr>  	<tr>    	<td>stripsites</td>    	</tr>  	<tr>    	<td>upgma</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/PAL/">http://bioweb.pasteur.fr/docs/PAL/</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/PAL/">/local/gensoft/doc/PAL</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>set PALDIR to /local/gensoft/lib/PAL and add  /local/gensoft/lib/PAL/share/pal.zip to CLASSPATH</td>       </tr>         </table>  	<p>  	<dt>	<a name=PALINGOL><i>PALINGOL</i> (1.3) 	<dd>	Un langage de programmation spcialis pour la  description de structures secondaires d'ADN.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>palamou</td>    	</tr>  	<tr>    	<td>galopin</td>      	<td><A HREF="/docs/man/doc/galopin.1">man galopin</a></td>    	</tr>  	<tr>    	<td>palingol</td>      	<td><A HREF="/docs/man/doc/palingol.1">man palingol</a></td>    	</tr>  	<tr>    	<td>galopin_main</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/palingol/doc//">/local/gensoft/doc/palingol/doc/</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/palingol/samples//">/local/gensoft/doc/palingol/samples/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=PAML><i>paml</i> (1.0) 	<dd>	A codon-based model of nucleotide substitution for protein-coding DNA sequences.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>baseml</td>    	</tr>  	<tr>    	<td>basemlg</td>    	</tr>  	<tr>    	<td>codeml</td>    	</tr>  	<tr>    	<td>pamp</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/paml//">/local/gensoft/doc/paml/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=PATHDB><i>PathDB</i> (1) 	<dd>	Une banque de chemins metaboliques.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>PathDB</td>    	</tr>  	</table>  	<p>  	<dt>	<a name=PAUP><i>PAUP</i> (4b10) 	<dd>	Phylogenetic Analysis Using Parsimony  Voir aussi : <a href="gensoft-evol.html#GCGPAUP">GCG PAUP</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>paup</td>      	<td><A HREF="/docs/man/doc/paup.1">man paup</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/paup//">/local/gensoft/doc/paup/</a></td></tr>      	<tr><td><A HREF="http://www.lms.si.edu/PAUP/support.html">http://www.lms.si.edu/PAUP/support.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=PDB2FASTA><i>pdb2fasta</i> (1) 	<dd>	Extracts the sequence from a PDB file.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>pdb2fasta</td>    	</tr>  	</table>  	<p>  	<dt>	<a name=PDBBROWSER><i>PDBBROWSER</i>  	<dd>	Recherche d'entres dans la Protein Data Bank.[X11]   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>pdbbrowse</td>      	<td><A HREF="/docs/man/doc/pdbbrowse.1">man pdbbrowse</a></td>    	</tr>  	</table>  	<p>  	<dt>	<a name=PDBSEARCH><i>pdbsearch</i> (1.0) 	<dd>	PDB database entries extraction.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>pdbsearch</td>      	<td><A HREF="/docs/man/man/pdbsearch.1.html">man pdbsearch</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/pdbsearch.html">pdbsearch</a></td></tr>    	</table>  	<p>  	<dt>	<a name=PDBTOOL><i>PDBtool</i> (2.0) 	<dd>	Recherche et analyse de structures macromolculaires d'entres de PDB.[X11]   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>PDBtool</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www.cse.ogi.edu/DISC/PDBTool/">http://www.cse.ogi.edu/DISC/PDBTool/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=PESTFIND><i>PESTFIND</i> (1-NOV-1995) 	<dd>	Recherche de rgions P, E, S et T (proline, acide glutamique, serine et threonine).   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>pestfind</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/pestfind-simple.html">PESTFIND</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www.icnet.uk/LRITu/projects/pest/">http://www.icnet.uk/LRITu/projects/pest/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=PFTOOLS><i>PFTOOLS</i> (2.2) 	<dd>	Recherche de profils dans des squences, et outils de conversion.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>gtop</td>      	<td><A HREF="/docs/man/man/gtop.1.html">man gtop</a></td>    	</tr>  	<tr>    	<td>pfsearch</td>      	<td><A HREF="/docs/man/man/pfsearch.1.html">man pfsearch</a></td>    	</tr>  	<tr>    	<td>pfscan</td>      	<td><A HREF="/docs/man/man/pfscan.1.html">man pfscan</a></td>    	</tr>  	<tr>    	<td>psa2msa</td>      	<td><A HREF="/docs/man/man/psa2msa.1.html">man psa2msa</a></td>    	</tr>  	<tr>    	<td>pfmake</td>      	<td><A HREF="/docs/man/man/pfmake.1.html">man pfmake</a></td>    	</tr>  	<tr>    	<td>pfw</td>      	<td><A HREF="/docs/man/man/pfw.1.html">man pfw</a></td>    	</tr>  	<tr>    	<td>ptoh</td>      	<td><A HREF="/docs/man/man/ptoh.1.html">man ptoh</a></td>    	</tr>  	<tr>    	<td>htop</td>      	<td><A HREF="/docs/man/man/htop.1.html">man htop</a></td>    	</tr>  	<tr>    	<td>pfscale</td>      	<td><A HREF="/docs/man/man/pfscale.1.html">man pfscale</a></td>    	</tr>  	<tr>    	<td>ptof</td>      	<td><A HREF="/docs/man/man/ptof.1.html">man ptof</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/pftools.html">PFTOOLS</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www.isrec.isb-sib.ch/sib-isrec/pftools/">http://www.isrec.isb-sib.ch/sib-isrec/pftools/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=PHRAP><i>Phrap</i> (0.990329) 	<dd>	Assemblage de fragments lus par Phred.  Voir aussi : <a href="gensoft-map.html#PHRED">Phred</a>, <a href="gensoft-map.html#CONSED">Consed</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>phrap</td>      	<td><A HREF="/docs/man/doc/phrap.1">man phrap</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td><A HREF="/docs/man/doc/phredPhrap.1">man phredPhrap</a></td></tr>      	<tr><td><A HREF="/docs/man/doc/swat.1">man swat</a></td></tr>      	<tr><td><A HREF="/docs/man/doc/cross_match.1">man cross_match</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/Phrap//">/local/gensoft/doc/Phrap/</a></td></tr>      	<tr><td><A HREF="http://bozeman.mbt.washington.edu/">http://bozeman.mbt.washington.edu/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=PHRED><i>Phred</i> (000925.c) 	<dd>	Lecteur de fichiers trace, base-calling et calcul de qualit  Voir aussi : <a href="gensoft-map.html#PHRAP">Phrap</a>, <a href="gensoft-map.html#CONSED">Consed</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>phred</td>      	<td><A HREF="/docs/man/doc/phred.1">man phred</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td><A HREF="/docs/man/doc/phredPhrap.1">man phredPhrap</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/Phred/NEWS">/local/gensoft/doc/Phred/NEWS</a></td></tr>      	<tr><td><A HREF="http://bozeman.mbt.washington.edu/">http://bozeman.mbt.washington.edu/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=PHYLIP><i>PHYLIP</i> (3.6a3) 	<dd>	Analyses phylogntiques.   Voir aussi : <a href="gensoft-evol.html#FASTDNAML">FASTDNAML</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>clique</td>      	<td><A HREF="/docs/man/doc/clique.1">man clique</a></td>    	</tr>  	<tr>    	<td>consense</td>      	<td><A HREF="/docs/man/doc/consense.1">man consense</a></td>    	</tr>  	<tr>    	<td>contml</td>      	<td><A HREF="/docs/man/doc/contml.1">man contml</a></td>    	</tr>  	<tr>    	<td>contrast</td>      	<td><A HREF="/docs/man/doc/contrast.1">man contrast</a></td>    	</tr>  	<tr>    	<td>dnacomp</td>      	<td><A HREF="/docs/man/doc/dnacomp.1">man dnacomp</a></td>    	</tr>  	<tr>    	<td>dnadist</td>      	<td><A HREF="/docs/man/doc/dnadist.1">man dnadist</a></td>    	</tr>  	<tr>    	<td>dnainvar</td>      	<td><A HREF="/docs/man/doc/dnainvar.1">man dnainvar</a></td>    	</tr>  	<tr>    	<td>dnaml</td>      	<td><A HREF="/docs/man/doc/dnaml.1">man dnaml</a></td>    	</tr>  	<tr>    	<td>dnamlk</td>      	<td><A HREF="/docs/man/doc/dnamlk.1">man dnamlk</a></td>    	</tr>  	<tr>    	<td>dnamove</td>      	<td><A HREF="/docs/man/doc/dnamove.1">man dnamove</a></td>    	</tr>  	<tr>    	<td>dnapars</td>      	<td><A HREF="/docs/man/doc/dnapars.1">man dnapars</a></td>    	</tr>  	<tr>    	<td>dnapenny</td>      	<td><A HREF="/docs/man/doc/dnapenny.1">man dnapenny</a></td>    	</tr>  	<tr>    	<td>dollop</td>      	<td><A HREF="/docs/man/doc/dollop.1">man dollop</a></td>    	</tr>  	<tr>    	<td>dolmove</td>      	<td><A HREF="/docs/man/doc/dolmove.1">man dolmove</a></td>    	</tr>  	<tr>    	<td>dolpenny</td>      	<td><A HREF="/docs/man/doc/dolpenny.1">man dolpenny</a></td>    	</tr>  	<tr>    	<td>drawgram</td>      	<td><A HREF="/docs/man/doc/drawgram.1">man drawgram</a></td>    	</tr>  	<tr>    	<td>drawtree</td>      	<td><A HREF="/docs/man/doc/drawtree.1">man drawtree</a></td>    	</tr>  	<tr>    	<td>factor</td>      	<td><A HREF="/docs/man/doc/factor.1">man factor</a></td>    	</tr>  	<tr>    	<td>fitch</td>      	<td><A HREF="/docs/man/doc/fitch.1">man fitch</a></td>    	</tr>  	<tr>    	<td>gendist</td>      	<td><A HREF="/docs/man/doc/gendist.1">man gendist</a></td>    	</tr>  	<tr>    	<td>kitsch</td>      	<td><A HREF="/docs/man/doc/kitsch.1">man kitsch</a></td>    	</tr>  	<tr>    	<td>mix</td>      	<td><A HREF="/docs/man/doc/mix.1">man mix</a></td>    	</tr>  	<tr>    	<td>move</td>      	<td><A HREF="/docs/man/doc/move.1">man move</a></td>    	</tr>  	<tr>    	<td>neighbor</td>      	<td><A HREF="/docs/man/doc/neighbor.1">man neighbor</a></td>    	</tr>  	<tr>    	<td>pars</td>      	<td><A HREF="/docs/man/doc/pars.1">man pars</a></td>    	</tr>  	<tr>    	<td>penny</td>      	<td><A HREF="/docs/man/doc/penny.1">man penny</a></td>    	</tr>  	<tr>    	<td>proml</td>      	<td><A HREF="/docs/man/doc/proml.1">man proml</a></td>    	</tr>  	<tr>    	<td>promlk</td>      	<td><A HREF="/docs/man/doc/promlk.1">man promlk</a></td>    	</tr>  	<tr>    	<td>protdist</td>      	<td><A HREF="/docs/man/doc/protdist.1">man protdist</a></td>    	</tr>  	<tr>    	<td>protpars</td>      	<td><A HREF="/docs/man/doc/protpars.1">man protpars</a></td>    	</tr>  	<tr>    	<td>restdist</td>      	<td><A HREF="/docs/man/doc/restdist.1">man restdist</a></td>    	</tr>  	<tr>    	<td>restml</td>      	<td><A HREF="/docs/man/doc/restml.1">man restml</a></td>    	</tr>  	<tr>    	<td>retree</td>      	<td><A HREF="/docs/man/doc/retree.1">man retree</a></td>    	</tr>  	<tr>    	<td>seqboot</td>      	<td><A HREF="/docs/man/doc/seqboot.1">man seqboot</a></td>    	</tr>  	<tr>    	<td>treedist</td>      	<td><A HREF="/docs/man/doc/treedist.1">man treedist</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td><A HREF="/docs/man/doc/contchar.1">man contchar</a></td></tr>      	<tr><td><A HREF="/docs/man/doc/discrete.1">man discrete</a></td></tr>      	<tr><td><A HREF="/docs/man/doc/distance.1">man distance</a></td></tr>      	<tr><td><A HREF="/docs/man/doc/draw.1">man draw</a></td></tr>      	<tr><td><A HREF="/docs/man/doc/phylip.1">man phylip</a></td></tr>      	<tr><td><A HREF="/docs/man/doc/sequence.1">man sequence</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/phylogeny/phylip-fr.html">PHYLIP</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://evolution.genetics.washington.edu/phylip.html">http://evolution.genetics.washington.edu/phylip.html</a></td></tr>      	<tr><td><A HREF="http://evolution.genetics.washington.edu/phylip/faq.html">http://evolution.genetics.washington.edu/phylip/faq.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>Version Macintosh: <A HREF="ftp://ftp.pasteur.fr/pub/GenSoft/Macintosh/evolution/">ftp://ftp.pasteur.fr/pub/GenSoft/Macintosh/evolution/</A></td>       </tr>         </table>  	<p>  	<dt>	<a name=PHYLO_WIN><i>PHYLO_WIN</i> (1.2) 	<dd>	Interface graphique pour la phylognie.[X11]  Voir aussi : <a href="gensoft-algt.html#SEAVIEW">SEAVIEW</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>phylo_win</td>      	<td><A HREF="/docs/man/doc/phylo_win.1">man phylo_win</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://pbil.univ-lyon1.fr/software/phylowin.html">http://pbil.univ-lyon1.fr/software/phylowin.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>Accepte les formats fasta, clustalw, PHYLIP et MASE. Le format MASE peut etre obtenu par SEAVIEW.</td>       </tr>         </table>  	<p>  	<dt>	<a name=PHYLODENDRON><i>phylodendron</i> (0.8d) 	<dd>	Phylogenetic tree drawing (also named TreeApp)   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>TreeApp</td>    	</tr>  	<tr>    	<td>phylodendron</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="http://iubio.bio.indiana.edu/treeapp/">phylodendron</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/TreeApp//">/local/gensoft/doc/TreeApp/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=PHYLOQUART><i>PHYLOQUART</i> (1.3) 	<dd>	A collection of programs aimed at estimating phylogenies from a quartet principle. The idea is to proceed in two steps: i) every set of four species is considered and one (or none) of the three possible bifuracting trees is chosen; ii) the 'quartets' (or trees on four species) are combined in an overall tree on the entire set of species.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>qstar</td>      	<td><A HREF="/docs/man/doc/qstar.1">man qstar</a></td>    	</tr>  	<tr>    	<td>distquart</td>      	<td><A HREF="/docs/man/doc/distquart.1">man distquart</a></td>    	</tr>  	<tr>    	<td>parciquart</td>      	<td><A HREF="/docs/man/doc/parciquart.1">man parciquart</a></td>    	</tr>  	<tr>    	<td>tree-pop</td>      	<td><A HREF="/docs/man/doc/tree-pop.1">man tree-pop</a></td>    	</tr>  	<tr>    	<td>addquart</td>      	<td><A HREF="/docs/man/doc/addquart.1">man addquart</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td><A HREF="/docs/man/doc/phyloquart.1">man phyloquart</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/phylogeny/phyloquart-fr.html">PHYLOQUART</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/PHYLOQUART/">/local/gensoft/doc/PHYLOQUART</a></td></tr>    	</table>  	<p>  	<dt>	<a name=PIMA><i>PIMA</i> (1.40) 	<dd>	Alignements multiples induits par motifs.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>print-cluster</td>    	</tr>  	<tr>    	<td>print-pima</td>      	<td><A HREF="/docs/man/man/print-pima.1.html">man print-pima</a></td>    	</tr>  	<tr>    	<td>make-pattern</td>    	</tr>  	<tr>    	<td>make-cluster</td>    	</tr>  	<tr>    	<td>pima</td>      	<td><A HREF="/docs/man/man/pima.1.html">man pima</a></td>    	</tr>  	<tr>    	<td>pima-gde</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/pima//">/local/gensoft/doc/pima/</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/pima/doc/pima.help">/local/gensoft/doc/pima/doc/pima.help</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/pima/doc/PIMA-PAPER/">/local/gensoft/doc/pima/doc/PIMA-PAPER</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/pima/tests//">/local/gensoft/doc/pima/tests/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=PISEJOB><i>pisejob</i>  	<dd>	bioweb jobs automatization   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>  	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>pisejob</td></tr>    	</table>  	<p>  	<dt>	<a name=PLSEARCH><i>PLSEARCH</i> (4.2) 	<dd>	Recherche de motifs AACC dans des squences protiques.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>IG-to-tbl</td>    	</tr>  	<tr>    	<td>tbl-to-IG</td>    	</tr>  	<tr>    	<td>plsearch</td>      	<td><A HREF="/docs/man/doc/plsearch.1">man plsearch</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/plsearch-simple.html">PLSEARCH</a></td></tr>    	</table>  	<p>  	<dt>	<a name=PRATT><i>PRATT</i> (2.0) 	<dd>	Recherche de rgions conserves par dtection de motifs flexibles dans un alignement. MDL-Pratt permet de trouver des sous-familles par approximation du meilleur ensemble de motifs (MDL : minimum description length).   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>pratt</td>      	<td><A HREF="/docs/man/doc/pratt.1">man pratt</a></td>    	</tr>  	<tr>    	<td>MDL-Pratt</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>pratt -h</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/motif/pratt/pratt-form.html">PRATT</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www.ii.uib.no/~inge/Pratt.html">http://www.ii.uib.no/~inge/Pratt.html</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/pratt//">/local/gensoft/doc/pratt/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=PREDATOR><i>predator</i> (2.1.2) 	<dd>	PREDATOR is a secondary structure prediction program. It takes as input a single protein sequence to be predicted and can optimally use a set of unaligned sequences as additional information to predict the query sequence.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>predator</td>      	<td><A HREF="/docs/man/doc/predator.1">man predator</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/predator-simple.html">predator</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/predator/">/local/gensoft/doc/predator</a></td></tr>    	</table>  	<p>  	<dt>	<a name=PRIMER0.5><i>primer0.5</i> (0.5) 	<dd>	Selection d'amorces pour PCR.   Voir aussi : <a href="#PRIMO">PRIMO</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>primer0.5</td>      	<td><A HREF="/docs/man/doc/primer0.5.1">man primer0.5</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/primer_0.5/manual.asc">/local/gensoft/doc/primer_0.5/manual.asc</a></td></tr>    	</table>  	<p>  	<dt>	<a name=PRIMER3><i>primer3</i> (3_0_9) 	<dd>	Selection d'amorces pour PCR.     	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>primer3</td>      	<td><A HREF="/docs/man/doc/primer3.1">man primer3</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="http://www.genome.wi.mit.edu/cgi-bin/primer/primer3_www.cgi">primer3</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/primer3/example">/local/gensoft/doc/primer3/example</a></td></tr>    	</table>  	<p>  	<dt>	<a name=PRIMO><i>primo</i> (1) 	<dd>	Conception de primers. Inspir de primer0.5 du MIT.  Voir aussi : <a href="#PRIMER0.5">PRIMER0.5</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>primo</td>      	<td><A HREF="/docs/man/doc/primo.1">man primo</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/primo.html">primo</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/primo/example//">/local/gensoft/doc/primo/example/</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>The environment variable : PRIMER_DEFAULTS may be set to a directory containing custom oligo.screen and human.rep files (see the example directory).</td>       </tr>         </table>  	<p>  	<dt>	<a name=PROCHECK><i>procheck</i> (3.5) 	<dd>	Programs to check the Stereochemical Quality of Protein Structures.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>aquapro</td>    	</tr>  	<tr>    	<td>gfac2pdb</td>    	</tr>  	<tr>    	<td>procheck</td>    	</tr>  	<tr>    	<td>procheck_comp</td>    	</tr>  	<tr>    	<td>procheck_nmr</td>    	</tr>  	<tr>    	<td>procomp</td>    	</tr>  	<tr>    	<td>proplot</td>    	</tr>  	<tr>    	<td>proplot_comp</td>    	</tr>  	<tr>    	<td>proplot_nmr</td>    	</tr>  	<tr>    	<td>viol2pdb</td>    	</tr>  	<tr>    	<td>wirplot</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/procheck/manual/">/local/gensoft/doc/procheck/manual</a></td></tr>    	</table>  	<p>  	<dt>	<a name=PROFIT><i>ProFit</i> (1.8) 	<dd>	Protein least squares fitting. (Andrew C.R. Martin)    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>profit</td>      	<td><A HREF="/docs/man/doc/profit.1">man profit</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>ProFit V1.8 has now been released. This new version includes a number of minor         enhancements and bug fixes over earlier versions. Enhancements: - Atoms with B-Values         less than a cutoff may be ignored and the selection of atoms to ignore on the basis of B-value         may be restricted to the mobile or reference structure - Missing atoms may be ignored         (generating a warning message) rather than generating an error - The number of fitted         atom pairs can be reported - The RESIDUE and WRITE commands can now output to a         pipe - Warns if a PDB file has multiple occupancies - Output uses CD1 for ILE rather than         CD Bug fixes: - Completely blank lines in PDB files resulted in the previous line of data being         duplicated. Fixed. - Fixed ore dump on PDB files with mutiple occupancy where the 'same'         atoms do not appear consecutively. - Fixed a problem when reading alignments where a         single residue was aligned an invalid zone would be created. </td>       </tr>         </table>  	<p>  	<dt>	<a name=PROMOTERSCAN><i>PROMOTER SCAN</i>  	<dd>	Recherche de squences promoteurs Pol II dans une squence.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>proscan</td>      	<td><A HREF="/docs/man/doc/proscan.1">man proscan</a></td>    	</tr>  	</table>  	<p>  	<dt>	<a name=PROSE><i>prose</i> (0.02) 	<dd>	Search for prosite patterns in protein  sequences.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>prose</td>      	<td><A HREF="/docs/man/man/prose.1.html">man prose</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/prose.html">prose</a></td></tr>    	</table>  	<p>  	<dt>	<a name=PROSEARCH><i>PROSEARCH</i> (2.1) 	<dd>	Recherche de motifs PROSITE dans une squence.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>prosearch</td>      	<td><A HREF="/docs/man/man/prosearch.1.html">man prosearch</a></td>    	</tr>  	<tr>    	<td>cregex</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/prosearch-simple.html">PROSEARCH</a></td></tr>    	</table>  	<p>  	<dt>	<a name=PROSITE><i>PROSITE</i> (2.1.4) 	<dd>	Recherche de motifs dans PROSITE (Hartmuth).   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>prosite</td>      	<td><A HREF="/docs/man/doc/prosite.1">man prosite</a></td>    	</tr>  	</table>  	<p>  	<dt>	<a name=PROTAL2DNA><i>protal2dna</i> (2.0) 	<dd>	Align the DNA sequences corresponding to their proteic  alignment.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>protal2dna</td>      	<td><A HREF="/docs/man/man/protal2dna.1.html">man protal2dna</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>protal2dna -h</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/protal2dna.html">protal2dna</a></td></tr>    	</table>  	<p>  	<dt>	<a name=PSORT><i>psort</i> (II) 	<dd>	PSORT II: a program to predict protein subcellular localization sites           from their amino acid sequences   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>psort</td>      	<td><A HREF="/docs/man/doc/psort.1">man psort</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/psort2.html">psort</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/psort/helpwww2.html">http://bioweb.pasteur.fr/docs/psort/helpwww2.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=PUZZLE><i>Puzzle</i> (5.0) 	<dd>	Recherche de topologies par test de maximum de vraisemblance. Cartes de vraisemblance.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>Puzzle</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/Puzzle.html">Puzzle</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/puzzle/manual.html">/local/gensoft/doc/puzzle/manual.html</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/puzzle/data/">/local/gensoft/doc/puzzle/data</a></td></tr>      	<tr><td><A HREF="http://www.tree-puzzle.de/">http://www.tree-puzzle.de/</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>Version Macintosh: <A HREF="ftp://ftp.pasteur.fr/pub/GenSoft/Macintosh/evolution/">ftp://ftp.pasteur.fr/pub/GenSoft/Macintosh/evolution/</A></td>       </tr>         </table>  	<p>  	<dt>	<a name=PYRAMIDS><i>PYRAMIDS</i> (2) 	<dd>	A pyramidal analysis tool for sequence clustering.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>pyramids</td>      	<td><A HREF="/docs/man/doc/pyramids.1">man pyramids</a></td>    	</tr>  	<tr>    	<td>drawpyr</td>    	</tr>  	<tr>    	<td>pyreval</td>    	</tr>  	<tr>    	<td>edlib</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>drawpyr -h</td></tr>      	<tr><td>pyreval -v</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/pyramids-simple.html">PYRAMIDS</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://genome.genetique.uvsq.fr/Pyramids/index.html">http://genome.genetique.uvsq.fr/Pyramids/index.html</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/pyramids/QuickStart">/local/gensoft/doc/pyramids/QuickStart</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/pyramids//">/local/gensoft/doc/pyramids/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=QR2><i>QR2</i> (1.0) 	<dd>	Approximation de dissimilarits non mtriques par  des distances d'arbres.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>qr2</td>      	<td><A HREF="/docs/man/doc/qr2.1">man qr2</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/qr2-simple.html">QR2</a></td></tr>    	</table>  	<p>  	<dt>	<a name=QTDT><i>qtdt</i> (2.2.1) 	<dd>	QTDT provides a convenient one-stop interface for family based tests of linkage disequilibrium. The general model described by Abecasis (2000) aplies to families with and without parental data, and includes an optional permutation framework for exact p-values. The tests described by Alllison (TDTQ5, 1997), Rabinowitz (1997), Monks (1998) and Fulker (1999) are also supported.  Voir aussi : <a href="gensoft-genet.html#SIMWALK2">simwalk2</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>qtdt</td>    	</tr>  	<tr>    	<td>prelude</td>    	</tr>  	<tr>    	<td>final</td>    	</tr>  	<tr>    	<td>pedstats</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>man qstat</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www.well.ox.ac.uk/asthma/QTDT/tour/index.html">http://www.well.ox.ac.uk/asthma/QTDT/tour/index.html</a></td></tr>      	<tr><td><A HREF="http://www.well.ox.ac.uk/asthma/QTDT/docs/index.html">http://www.well.ox.ac.uk/asthma/QTDT/docs/index.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=QTLCARTOGRAPHER><i>QTLCartographer</i> (1.12d) 	<dd>	Localisation de gnes de traits quantitatifs par une carte de marqueurs.   Voir aussi : <a href="gensoft-genet.html#MAPMAKER">MAPMAKER</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>Rmap</td>      	<td><A HREF="/docs/man/man/Rmap.1.html">man Rmap</a></td>    	</tr>  	<tr>    	<td>Rqtl</td>      	<td><A HREF="/docs/man/man/Rqtl.1.html">man Rqtl</a></td>    	</tr>  	<tr>    	<td>Eqtl</td>      	<td><A HREF="/docs/man/man/Eqtl.1.html">man Eqtl</a></td>    	</tr>  	<tr>    	<td>Rcross</td>      	<td><A HREF="/docs/man/man/Rcross.1.html">man Rcross</a></td>    	</tr>  	<tr>    	<td>Qstats</td>      	<td><A HREF="/docs/man/man/Qstats.1.html">man Qstats</a></td>    	</tr>  	<tr>    	<td>LRmapqtl</td>      	<td><A HREF="/docs/man/man/LRmapqtl.1.html">man LRmapqtl</a></td>    	</tr>  	<tr>    	<td>Zmapqtl</td>      	<td><A HREF="/docs/man/man/Zmapqtl.1.html">man Zmapqtl</a></td>    	</tr>  	<tr>    	<td>QTLcart</td>      	<td><A HREF="/docs/man/man/QTLcart.1.html">man QTLcart</a></td>    	</tr>  	<tr>    	<td>Preplot</td>      	<td><A HREF="/docs/man/man/Preplot.1.html">man Preplot</a></td>    	</tr>  	<tr>    	<td>Prune</td>      	<td><A HREF="/docs/man/man/Prune.1.html">man Prune</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/QTLCart/doc/">/local/gensoft/doc/QTLCart/doc</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/QTLCart/example/">/local/gensoft/doc/QTLCart/example</a></td></tr>    	</table>  	<p>  	<dt>	<a name=QTREE><i>QTree</i> (2.1) 	<dd>	Gnration d'images  partir d'entres de PDB. Les images produites sont des fichiers au format MTV visibles et ditables par ImageMagick (man ImageMagick).   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>qtree</td>      	<td><A HREF="/docs/man/doc/qtree.1">man qtree</a></td>    	</tr>  	<tr>    	<td>worms</td>    	</tr>  	<tr>    	<td>ballstick</td>    	</tr>  	<tr>    	<td>cpk</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>qtree -h</td></tr>      	<tr><td>worms -h</td></tr>      	<tr><td>ballstick -h</td></tr>      	<tr><td>cpk -h</td></tr>    	</table>  	<p>  	<dt>	<a name=QUICKTREE><i>quicktree</i> (1) 	<dd>	A program for the rapid reconstruction of phylogenies by the Neighbor-Joining method.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>quicktree</td>      	<td><A HREF="/docs/man/doc/quicktree.1">man quicktree</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/quicktree.html">quicktree</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www.sanger.ac.uk/Software/analysis/quicktree/">http://www.sanger.ac.uk/Software/analysis/quicktree/</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/quicktree/">/local/gensoft/doc/quicktree</a></td></tr>    	</table>  	<p>  	<dt>	<a name=RASMOL><i>RASMOL</i> (2.6b2) 	<dd>	Visualisation en modlisation molculaire.[X11]   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>rasmol</td>      	<td><A HREF="/docs/man/man/rasmol.1.html">man rasmol</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www.bio.cam.ac.uk/doc/rasmol.html">http://www.bio.cam.ac.uk/doc/rasmol.html</a></td></tr>      	<tr><td><A HREF="http://www.umass.edu/microbio/rasmol/">http://www.umass.edu/microbio/rasmol/</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>Disponible galement sur les stations Silicon  Graphics du SIS.  Version Macintosh: <A HREF="ftp://ftp.pasteur.fr/pub/GenSoft/Macintosh/molecular_graphics/">ftp://ftp.pasteur.fr/pub/GenSoft/Macintosh/molecular_graphics/</A></td>       </tr>         </table>  	<p>  	<dt>	<a name=RASTER3D><i>Raster3D</i> (2.4j) 	<dd>	Generer les images de proteins ou de autres molecules.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>balls</td>      	<td><A HREF="/docs/man/man/balls.l.html">man balls</a></td>    	</tr>  	<tr>    	<td>normal3d</td>      	<td>man normal3d</td>    	</tr>  	<tr>    	<td>rastep</td>      	<td>man rastep</td>    	</tr>  	<tr>    	<td>rods</td>      	<td><A HREF="/docs/man/man/rods.l.html">man rods</a></td>    	</tr>  	<tr>    	<td>ribbon</td>      	<td><A HREF="/docs/man/man/ribbon.l.html">man ribbon</a></td>    	</tr>  	<tr>    	<td>render</td>      	<td><A HREF="/docs/man/man/render.l.html">man render</a></td>    	</tr>  	<tr>    	<td>avs2ps</td>      	<td><A HREF="/docs/man/man/avs2ps.l.html">man avs2ps</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/raster3d//">/local/gensoft/doc/raster3d/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=READNEXUS><i>readnexus</i> (1.4) 	<dd>	Convert NEXUS files (from PAUP or MacClade) into  fasta or mega format.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>readnexus</td>    	</tr>  	</table>  	<p>  	<dt>	<a name=READSEQ><i>READSEQ</i> (2.0.6) 	<dd>	Conversions de formats. Brin complmentaire.  Voir aussi : <a href="gensoft-tools.html#FMTSEQ">fmtseq</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>readseq</td>      	<td>man readseq</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/readseq-simple.html">READSEQ</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/readseq-help.html">http://bioweb.pasteur.fr/docs/readseq-help.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=READSEQ2><i>readseq2</i> (2.1.6) 	<dd>	Conversion de formats.  Extraction de features.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>readseq2</td>      	<td><A HREF="/docs/man/doc/readseq2.1">man readseq2</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/cgi-bin/readseq2/readseq.cgi">readseq2</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/cgi-bin/readseq2/readseq.cgi">http://bioweb.pasteur.fr/cgi-bin/readseq2/readseq.cgi</a></td></tr>      	<tr><td><A HREF="/cgi-bin/readseq2/readseq.cgi?morehelp">http://bioweb.pasteur.fr/cgi-bin/readseq2/readseq.cgi?morehelp</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>version java  changement de numero de formats</td>       </tr>         </table>  	<p>  	<dt>	<a name=RECPARS><i>RecPars</i> (1) 	<dd>	RecPars does a parsimony analysis of DNA sequences. It tries to  find the best phylogenies for different regions of the sequences and thereby postulating a recombination event between these segments   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>RecPars</td>      	<td><A HREF="/docs/man/doc/RecPars.1">man RecPars</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/RecPars/">/local/gensoft/doc/RecPars</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/RecPars/example//">/local/gensoft/doc/RecPars/example/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=REPEATMASKER><i>RepeatMasker</i> (07262001) 	<dd>	A program that screens DNA sequences for low complexity DNA sequences and interspersed repeats.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>RepeatMasker</td>      	<td><A HREF="/docs/man/doc/RepeatMasker.1">man RepeatMasker</a></td>    	</tr>  	<tr>    	<td>rm2gb</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/RepeatMasker-simple.html">RepeatMasker</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>rm2gb extracts repeats as Genbank formatted  annotations.</td>       </tr>         </table>  	<p>  	<dt>	<a name=REPEATS><i>repeats</i> (1.1) 	<dd>	Trouve des motifs d'une taille allant de 1  32 nuclotides,  rpts en tandem, dans des squences d'acides nucliques.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>repeats</td>      	<td><A HREF="/docs/man/doc/repeats.1">man repeats</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/repeats.html">repeats</a></td></tr>    	</table>  	<p>  	<dt>	<a name=REPUTER><i>reputer</i> (2) 	<dd>	Fast Computation of Maximal Repeats in Complete Genomes   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>reputer</td>      	<td><A HREF="/docs/man/doc/reputer.1">man reputer</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/reputer-simple.html">reputer</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/reputer//">/local/gensoft/doc/reputer/</a></td></tr>      	<tr><td><A HREF="http://bibiserv.techfak.uni-bielefeld.de/reputer/">http://bibiserv.techfak.uni-bielefeld.de/reputer/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=RESTMAP><i>RESTMAP</i> (May, 1992) 	<dd>	Cartes de restriction.   Voir aussi : <a href="gensoft-na.html#TACG">TACG</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>mapc</td>    	</tr>  	<tr>    	<td>mapl</td>    	</tr>  	<tr>    	<td>diged</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td><A HREF="/docs/man/doc/restmap.1">man restmap</a></td></tr>    	</table>  	<p>  	<dt>	<a name=RNABOB><i>RNABOB</i> (2.1) 	<dd>	Recherche de motifs d'ARN dans une banque de squences.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>rnabob</td>      	<td><A HREF="/docs/man/man/rnabob.1.html">man rnabob</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/rnabob/rnabob.ps">/local/gensoft/doc/rnabob/rnabob.ps</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/rnabob//">/local/gensoft/doc/rnabob/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=RNAGA><i>rnaga</i> (1) 	<dd>	Prediction of common secondary structures of RNAs by genetic algorithm   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>rnaga</td>      	<td><A HREF="/docs/man/doc/rnaga.1">man rnaga</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/rnaga.html">rnaga</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/rnaga/">/local/gensoft/doc/rnaga</a></td></tr>    	</table>  	<p>  	<dt>	<a name=SAM><i>SAM</i> (3.2.1) 	<dd>	Modeles de Markov (HMM) pour l'alignement de sequences.   Voir aussi : <a href="#HMMER">HMMER</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>align2model</td>    	</tr>  	<tr>    	<td>build-weighted-model</td>    	</tr>  	<tr>    	<td>buildmodel</td>    	</tr>  	<tr>    	<td>checkseq</td>    	</tr>  	<tr>    	<td>convertmodel.pl</td>    	</tr>  	<tr>    	<td>dbletters</td>    	</tr>  	<tr>    	<td>drawmodel</td>    	</tr>  	<tr>    	<td>fh0.3</td>    	</tr>  	<tr>    	<td>fh0.5</td>    	</tr>  	<tr>    	<td>fw0.1</td>    	</tr>  	<tr>    	<td>fw0.2</td>    	</tr>  	<tr>    	<td>fw0.3</td>    	</tr>  	<tr>    	<td>fw0.5</td>    	</tr>  	<tr>    	<td>fw0.7</td>    	</tr>  	<tr>    	<td>fw0.8</td>    	</tr>  	<tr>    	<td>fw1.0</td>    	</tr>  	<tr>    	<td>grabdp</td>    	</tr>  	<tr>    	<td>hmmer2sam</td>    	</tr>  	<tr>    	<td>hmmscore</td>    	</tr>  	<tr>    	<td>make_template</td>    	</tr>  	<tr>    	<td>makehist</td>    	</tr>  	<tr>    	<td>makeroc</td>    	</tr>  	<tr>    	<td>makeroc2</td>    	</tr>  	<tr>    	<td>makeroc3</td>    	</tr>  	<tr>    	<td>makeroc4</td>    	</tr>  	<tr>    	<td>modelfromalign</td>    	</tr>  	<tr>    	<td>modifymodel</td>    	</tr>  	<tr>    	<td>multi_roc2.pl</td>    	</tr>  	<tr>    	<td>permuteseq</td>    	</tr>  	<tr>    	<td>prettyalign</td>    	</tr>  	<tr>    	<td>readseq.sam</td>    	</tr>  	<tr>    	<td>sam2hmmer</td>    	</tr>  	<tr>    	<td>sampleseqs</td>    	</tr>  	<tr>    	<td>sortseq</td>    	</tr>  	<tr>    	<td>target99</td>    	</tr>  	<tr>    	<td>uniqueseq</td>    	</tr>  	<tr>    	<td>varh50</td>    	</tr>  	<tr>    	<td>w0.5</td>    	</tr>  	<tr>    	<td>hmmconvert.sam</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/motif/sam-fr.html">SAM</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/sam/sam_doc.ps">/local/gensoft/doc/sam/sam_doc.ps</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/sam/sam-demos/">/local/gensoft/doc/sam/sam-demos</a></td></tr>      	<tr><td><A HREF="/docs/sam/">http://bioweb.pasteur.fr/docs/sam/</a></td></tr>      	<tr><td><A HREF="http://www.cse.ucsc.edu/research/compbio/sam.html">http://www.cse.ucsc.edu/research/compbio/sam.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=SAPS><i>SAPS</i> (11-05-93) 	<dd>	(Statistical Analysis of Protein Squences) Analyses diverses : biais de composition, structures repetitives, ...   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>saps</td>      	<td><A HREF="/docs/man/man/saps.1.html">man saps</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/saps-simple.html">SAPS</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/SAPS//">/local/gensoft/doc/SAPS/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=SATELLITES><i>satellites</i> (0.2) 	<dd>	Identifying satellites and periodic repetitions  in biological sequences.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>sat</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td><A HREF="/docs/man/doc/satellites.1">man satellites</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/satellites.html">satellites</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/satellites//">/local/gensoft/doc/satellites/</a></td></tr>      	<tr><td><A HREF="http://www-igm.univ-mlv.fr/~sagot/publications/satellites/jcb.ps">http://www-igm.univ-mlv.fr/~sagot/publications/satellites/jcb.ps</a></td></tr>    	</table>  	<p>  	<dt>	<a name=SC_RATE><i>SC_rate</i> (1.1) 	<dd>	Calcul d'indices de fiabilit pour un alignement de squences protines. (SC = sequence and composition).   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>sc_rate</td>      	<td><A HREF="/docs/man/doc/SC_rate.1">man SC_rate</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/SC_rate//">/local/gensoft/doc/SC_rate/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=SCAN_FOR_MATCHES><i>scan_for_matches</i>  	<dd>	Recherche de motifs dans des squences d'ADN ou de protines.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>show_hits</td>    	</tr>  	<tr>    	<td>scan_for_matches</td>      	<td><A HREF="/docs/man/doc/scan_for_matches.1">man scan_for_matches</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/scan_for_matches//">/local/gensoft/doc/scan_for_matches/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=SEAVIEW><i>SEAVIEW</i> (2000.06) 	<dd>	Outil graphique pour l'alignement de squences.[X11]   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>seaview</td>      	<td>man seaview</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://pbil.univ-lyon1.fr/software/seaview.html">http://pbil.univ-lyon1.fr/software/seaview.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=SEG><i>Seg</i> (199910) 	<dd>	Segmentation de squences par complxit locale.  Voir aussi : <a href="gensoft-tools.html#XNU">XNU</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>seg</td>      	<td><A HREF="/docs/man/man/seg.1.html">man seg</a></td>    	</tr>  	<tr>    	<td>pseg</td>    	</tr>  	<tr>    	<td>nseg</td>    	</tr>  	</table>  	<p>  	<dt>	<a name=SENSEI><i>SENSEI</i> (0.0) 	<dd>	SENsitive SEarch Implementation for Nucleic Acid  Sequence Similarity. Recherche de squences d'ADN similaires dans une banque (comme BLASTN mais optimis pour l'ADN).   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>sensei</td>      	<td><A HREF="/docs/man/doc/sensei.1">man sensei</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/sensei/sensei.ps">/local/gensoft/doc/sensei/sensei.ps</a></td></tr>    	</table>  	<p>  	<dt>	<a name=SEQGEN><i>Seq-Gen</i> (1.2.6) 	<dd>	Sequence-Generator: simulation par la mthode de  Monte-Carlo de l'volution de squences d'ADN sur des arbres phylogntiques.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>seq-gen</td>      	<td><A HREF="/docs/man/doc/Seq-Gen.1">man Seq-Gen</a></td>    	</tr>  	<tr>    	<td>phy2nex</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/seqgen-simple.html">Seq-Gen</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/Seq-Gen//">/local/gensoft/doc/Seq-Gen/</a></td></tr>      	<tr><td><A HREF="/docs/Seq-Gen/">http://bioweb.pasteur.fr/docs/Seq-Gen/</a></td></tr>      	<tr><td><A HREF="http://evolve.zoo.ox.ac.uk/software/Seq-Gen/main.html">http://evolve.zoo.ox.ac.uk/software/Seq-Gen/main.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>Version Macintosh: <A HREF="ftp://ftp.pasteur.fr/pub/GenSoft/Macintosh/evolution/">ftp://ftp.pasteur.fr/pub/GenSoft/Macintosh/evolution/</A></td>       </tr>         </table>  	<p>  	<dt>	<a name=SEQALN><i>SEQALN</i> (2.0) 	<dd>	Programmes d'alignement de squences : alignement global, local, recouvrement rptitions (M.S. Waterman). Pour les programmeurs, une librairie de fonctions d'alignement.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>fitD</td>      	<td><A HREF="/docs/man/man/fitD.1.html">man fitD</a></td>    	</tr>  	<tr>    	<td>fitS</td>      	<td><A HREF="/docs/man/man/fitS.1.html">man fitS</a></td>    	</tr>  	<tr>    	<td>globalD</td>      	<td><A HREF="/docs/man/man/globalD.1.html">man globalD</a></td>    	</tr>  	<tr>    	<td>globalS</td>      	<td><A HREF="/docs/man/man/globalS.1.html">man globalS</a></td>    	</tr>  	<tr>    	<td>localS</td>      	<td><A HREF="/docs/man/man/localS.1.html">man localS</a></td>    	</tr>  	<tr>    	<td>mfitD</td>      	<td><A HREF="/docs/man/man/mfitD.1.html">man mfitD</a></td>    	</tr>  	<tr>    	<td>mfitS</td>      	<td><A HREF="/docs/man/man/mfitS.1.html">man mfitS</a></td>    	</tr>  	<tr>    	<td>mglobalD</td>      	<td><A HREF="/docs/man/man/mglobalD.1.html">man mglobalD</a></td>    	</tr>  	<tr>    	<td>mglobalS</td>      	<td><A HREF="/docs/man/man/mglobalS.1.html">man mglobalS</a></td>    	</tr>  	<tr>    	<td>mlocalS</td>      	<td><A HREF="/docs/man/man/mlocalS.1.html">man mlocalS</a></td>    	</tr>  	<tr>    	<td>moverS</td>      	<td><A HREF="/docs/man/man/moverS.1.html">man moverS</a></td>    	</tr>  	<tr>    	<td>mpvlocalS</td>      	<td><A HREF="/docs/man/man/mpvlocalS.1.html">man mpvlocalS</a></td>    	</tr>  	<tr>    	<td>mpvsrlocalS</td>      	<td><A HREF="/docs/man/man/mpvsrlocalS.1.html">man mpvsrlocalS</a></td>    	</tr>  	<tr>    	<td>msrlocalS</td>      	<td><A HREF="/docs/man/man/msrlocalS.1.html">man msrlocalS</a></td>    	</tr>  	<tr>    	<td>mtrlocalS</td>      	<td><A HREF="/docs/man/man/mtrlocalS.1.html">man mtrlocalS</a></td>    	</tr>  	<tr>    	<td>overS</td>      	<td><A HREF="/docs/man/man/overS.1.html">man overS</a></td>    	</tr>  	<tr>    	<td>pfitS</td>      	<td><A HREF="/docs/man/man/pfitS.1.html">man pfitS</a></td>    	</tr>  	<tr>    	<td>pvlocalS</td>      	<td><A HREF="/docs/man/man/pvlocalS.1.html">man pvlocalS</a></td>    	</tr>  	<tr>    	<td>pvsrlocalS</td>      	<td><A HREF="/docs/man/man/pvsrlocalS.1.html">man pvsrlocalS</a></td>    	</tr>  	<tr>    	<td>srlocalS</td>      	<td><A HREF="/docs/man/man/srlocalS.1.html">man srlocalS</a></td>    	</tr>  	<tr>    	<td>trlocalS</td>      	<td><A HREF="/docs/man/man/trlocalS.1.html">man trlocalS</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td><A HREF="/docs/man/man/seqaln-intro.1.html">man seqaln-intro</a></td></tr>      	<tr><td><A HREF="/docs/man/man/libseqaln.3.html">man libseqaln</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="http://www-hto.usc.edu/software/seqaln/seqaln-query.html">SEQALN</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/seqaln/seqalndoc.ps">/local/gensoft/doc/seqaln/seqalndoc.ps</a></td></tr>      	<tr><td><A HREF="http://central.pasteur.fr/docs/seqaln/">http://central.pasteur.fr/docs/seqaln/</a></td></tr>      	<tr><td><A HREF="http://www-hto.usc.edu/software/seqaln/">http://www-hto.usc.edu/software/seqaln/</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/seqaln//">/local/gensoft/doc/seqaln/</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>Compile with -I/local/gensoft/include/seqaln</td>       </tr>         </table>  	<p>  	<dt>	<a name=SEQIO><i>SEQIO</i> (1.2.2) 	<dd>	Conversions de formats. Interface de programmation pour les entres-sorties de squences.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>fmtseq</td>      	<td><A HREF="/docs/man/doc/fmtseq.1">man fmtseq</a></td>    	</tr>  	<tr>    	<td>idxseq</td>      	<td><A HREF="/docs/man/doc/idxseq.1">man idxseq</a></td>    	</tr>  	<tr>    	<td>grepseq</td>    	</tr>  	<tr>    	<td>wcseq</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td><A HREF="/docs/man/doc/seqio.1">man seqio</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/seqio/">/local/gensoft/doc/seqio</a></td></tr>      	<tr><td><A HREF="/docs/seqio/seqio.html">http://bioweb.pasteur.fr/docs/seqio/seqio.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>Compile with: -I/local/gensoft/include. Link with /local/gensoft/lib/seqio/seqio.o</td>       </tr>         </table>  	<p>  	<dt>	<a name=SEQPUP><i>SEQPUP</i>  	<dd>	dition et analyses de squences. Alignements  multiples.[X11]   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>SeqPup</td>      	<td><A HREF="/docs/man/doc/seqpup.1">man seqpup</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>Version Macintosh: <A HREF="ftp://ftp.pasteur.fr/pub/GenSoft/Macintosh/sequence_tools">ftp://ftp.pasteur.fr/pub/GenSoft/Macintosh/sequence_tools</A></td>       </tr>         </table>  	<p>  	<dt>	<a name=SEQSBLAST><i>seqsblast</i> (3.1) 	<dd>	Extracts a given number of sequences from a Blast output.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>seqsblast</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/seqsblast.html">seqsblast</a></td></tr>    	</table>  	<p>  	<dt>	<a name=SEQSPLIT><i>seqsplit</i> (1.1) 	<dd>	Programs for running blastx on very long queries   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>seqsplit</td>    	</tr>  	<tr>    	<td>Blastunsplit</td>    	</tr>  	</table>  	<p>  	<dt>	<a name=SEQUIN><i>Sequin</i> (3.85) 	<dd>	Soumission de squences aux banques.[X11]   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>sequin</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www.ncbi.nlm.nih.gov/Sequin/">http://www.ncbi.nlm.nih.gov/Sequin/</a></td></tr>      	<tr><td><A HREF="http://www.ncbi.nlm.nih.gov/Sequin/QuickGuide/sequin.htm">http://www.ncbi.nlm.nih.gov/Sequin/QuickGuide/sequin.htm</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>Version Macintosh: <A HREF="ftp://ftp.pasteur.fr/pub/GenSoft/Macintosh/db_soft/">ftp://ftp.pasteur.fr/pub/GenSoft/Macintosh/db_soft/</A> Version Windows : ftp://ftp.pasteur.fr/pub/GenSoft/MS-Windows/db_soft/</td>       </tr>         </table>  	<p>  	<dt>	<a name=SEQUTILS><i>SeqUtils</i>  	<dd>	Perl sequence utilities.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>  	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>perldoc Gensoft::SeqUtils</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>use Gensoft::SeqUtils;</td>       </tr>         </table>  	<p>  	<dt>	<a name=SIGMA><i>SIGMA</i> (2.31) 	<dd>	Visualisation de cartes de chromosomes.[X11]   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>sigma</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/sigma/overview.ps">/local/gensoft/doc/sigma/overview.ps</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/sigma/viewing_tutorial.ps">/local/gensoft/doc/sigma/viewing_tutorial.ps</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/sigma//">/local/gensoft/doc/sigma/</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>Version Macintosh: <A HREF="ftp://ftp.pasteur.fr/pub/GenSoft/Macintosh/molecular_graphics/">ftp://ftp.pasteur.fr/pub/GenSoft/Macintosh/molecular_graphics/</A></td>       </tr>         </table>  	<p>  	<dt>	<a name=SIGNALSCAN><i>SIGNALSCAN</i> (4.07) 	<dd>	Analyse des signaux dans les squences ADN eukaryotes : facteurs de transcription (banques  TFD, TRANSFAC et IMD).   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>sigscan</td>      	<td><A HREF="/docs/man/doc/sigscan.1">man sigscan</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/sigscan//">/local/gensoft/doc/sigscan/</a></td></tr>      	<tr><td><A HREF="http://biosci.cbs.umn.edu/software/sigscan.html">http://biosci.cbs.umn.edu/software/sigscan.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=SIM><i>SIM</i> (2.5) 	<dd>	Alignement local Smith-Waterman. Affichage graphique avec LALNVIEW.  Voir aussi : <a href="gensoft-algt.html#LALNVIEW">LALNVIEW</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>sim</td>      	<td><A HREF="/docs/man/doc/sim.1">man sim</a></td>    	</tr>  	</table>  	<p>  	<dt>	<a name=SIMWALK2><i>simwalk2</i> (2.83) 	<dd>	SimWalk2 is a statistical genetics computer application for haplotype, parametric linkage, non-parametric linkage (NPL), identity by descent (IBD) and mistyping analyses on any size of pedigree. SimWalk2 uses Markov chain Monte Carlo (MCMC) and simulated annealing algorithms to perform these multipoint analyses.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>simwalk2</td>      	<td><A HREF="/docs/man/doc/simwalk2.1">man simwalk2</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/simwalk2">http://bioweb.pasteur.fr/docs/simwalk2</a></td></tr>    	</table>  	<p>  	<dt>	<a name=SLBC><i>SLBC</i> (2.7) 	<dd>	BCM Search Launcher Batch Client. The Search Launcher Batch Client (SLBC) will read-in multiple input files, perform a specified search (e.g., BLAST, BEAUTY) on each sequence (one at a time), then store the result files on the user's system as individual HTML documents. The search results can then be viewed using Netscape, MS Internet Explorer or another HTML viewer.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>bcm-search-launcher</td>    	</tr>  	<tr>    	<td>SLBC</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://dot.imgen.bcm.tmc.edu:9331/downloads/software/batch_client.html">http://dot.imgen.bcm.tmc.edu:9331/downloads/software/batch_client.html</a></td></tr>      	<tr><td><A HREF="http://dot.imgen.bcm.tmc.edu:9331/">http://dot.imgen.bcm.tmc.edu:9331/</a></td></tr>      	<tr><td><A HREF="http://dot.imgen.bcm.tmc.edu:9331/docs/sl_links.html">http://dot.imgen.bcm.tmc.edu:9331/docs/sl_links.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=SLINK><i>SLINK</i> (2.50) 	<dd>	Programme de simulation pour l'analyse de liaisons.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>slink</td>      	<td><A HREF="/docs/man/doc/slink.1">man slink</a></td>    	</tr>  	<tr>    	<td>isim</td>    	</tr>  	<tr>    	<td>lsim</td>    	</tr>  	<tr>    	<td>msim</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/linkage/slink/example1/">/local/gensoft/doc/linkage/slink/example1</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/linkage/slink/example2/">/local/gensoft/doc/linkage/slink/example2</a></td></tr>      	<tr><td><A HREF="http://linkage.rockefeller.edu/soft/slink.html">http://linkage.rockefeller.edu/soft/slink.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=SMILE><i>SMILE</i> (1.44) 	<dd>	Structured Motifs Inference and Evaluation. Inference of structured signals in multiple sequences   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>smile</td>      	<td><A HREF="/docs/man/man/SMILE.1.html">man SMILE</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/smile.html">SMILE</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www-igm.univ-mlv.fr/~marsan/smile_english.html">http://www-igm.univ-mlv.fr/~marsan/smile_english.html</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/SMILE//">/local/gensoft/doc/SMILE/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=SNAP><i>Snap</i> (1) 	<dd>	Synonymous Nonsynonymous Analysis Program This program calculates the number of synonymous vs. non-synonymous base substitutions as described in Nei and Gojobori for all pairwise comparisons of sequences in an alignment.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>snap</td>      	<td>man snap</td>    	</tr>  	<tr>    	<td>codons-xyplot</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/Snap/example/">/local/gensoft/doc/Snap/example</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/Snap//">/local/gensoft/doc/Snap/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=SOLAR><i>solar</i> (1.7.3) 	<dd>	SOLAR is a program for multipoint, oligogenic, variance component  linkage analysis in pedigrees of arbitrary size and complexity.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>solar</td>      	<td><A HREF="/docs/man/doc/solar.1">man solar</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/solar">http://bioweb.pasteur.fr/docs/solar</a></td></tr>      	<tr><td><A HREF="/docs/solar/Example">http://bioweb.pasteur.fr/docs/solar/Example</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>Il faut que l'utilisateur demande une cl  solar@darwin.sfbr.org pour utiliser le logiciel. Voir chapitre 2.3. Registering SOLAR </td>       </tr>         </table>  	<p>  	<dt>	<a name=SPLITBLAST><i>splitblast</i> (1) 	<dd>	Pour sparer les rsultats d'un Blast multiple.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>splitblast</td>    	</tr>  	</table>  	<p>  	<dt>	<a name=SPLITSTREE><i>SplitsTree</i> (2.4) 	<dd>	A Program for Analyzing and Visualizing Evolutionary Data.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>splits</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td><A HREF="/docs/man/doc/splitstree.1">man splitstree</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://bibiserv.techfak.uni-bielefeld.de/splits/">http://bibiserv.techfak.uni-bielefeld.de/splits/</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/splitstree/">/local/gensoft/doc/splitstree</a></td></tr>    	</table>  	<p>  	<dt>	<a name=SRS><i>SRS</i>  	<dd>	Recherche d'entres dans les banques de squences et de structures.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>  	</tr>  	<tr>  	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="http://srs.pasteur.fr/">SRS</a></td></tr>    	</table>  	<p>  	<dt>	<a name=STADEN><i>STADEN</i> (2001.0) 	<dd>	Outils d'analyse de squences. Assemblage de contigs.[X11]   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>  	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td><A HREF="/docs/man/doc/staden.4">man staden</a></td></tr>      	<tr><td><A HREF="/docs/man/man/makeSCF.1.html">man makeSCF</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/staden/">http://bioweb.pasteur.fr/docs/staden/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=STAMP><i>STAMP</i> (4.2) 	<dd>	Structural Alignment of Multiple Proteins  Voir aussi : <a href="gensoft-algt.html#ALSCRIPT">ALSCRIPT</a>, <a href="gensoft-algt.html#AMPS">AMPS</a>, <a href="gensoft-algt.html#AMAS">AMAS</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>alignfit</td>    	</tr>  	<tr>    	<td>avestruc</td>    	</tr>  	<tr>    	<td>dstamp</td>    	</tr>  	<tr>    	<td>extrans</td>    	</tr>  	<tr>    	<td>gstamp</td>    	</tr>  	<tr>    	<td>mergestamp</td>    	</tr>  	<tr>    	<td>mergetrans</td>    	</tr>  	<tr>    	<td>pdbc</td>    	</tr>  	<tr>    	<td>pdbseq</td>    	</tr>  	<tr>    	<td>pickframe</td>    	</tr>  	<tr>    	<td>poststamp</td>    	</tr>  	<tr>    	<td>sorttrans</td>    	</tr>  	<tr>    	<td>stamp</td>      	<td><A HREF="/docs/man/doc/stamp.1">man stamp</a></td>    	</tr>  	<tr>    	<td>stamp_clean</td>    	</tr>  	<tr>    	<td>transform</td>    	</tr>  	<tr>    	<td>ver2hor</td>    	</tr>  	<tr>    	<td>aconvert</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/structure/stamp-fr.html">STAMP</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/stamp/">http://bioweb.pasteur.fr/docs/stamp/</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/stamp/doc/stamp.ps">/local/gensoft/doc/stamp/doc/stamp.ps</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/stamp/examples//">/local/gensoft/doc/stamp/examples/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=STATA><i>STATA</i> (7.0) 	<dd>	Logiciel gnral de statistiques.[X11]   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>stata</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www.stata.com/">http://www.stata.com/</a></td></tr>      	<tr><td><A HREF="http://www.stata.com/support/faqs/">http://www.stata.com/support/faqs/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=STATALIGN><i>STATALIGN</i>  	<dd>	Alignements avec modles volutifs explicites.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>statdna</td>    	</tr>  	<tr>    	<td>statdnaC</td>    	</tr>  	<tr>    	<td>statprot</td>    	</tr>  	<tr>    	<td>statprotC</td>    	</tr>  	<tr>    	<td>arcs2cps</td>    	</tr>  	<tr>    	<td>arcs2bwps</td>    	</tr>  	<tr>    	<td>medians</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td><A HREF="/docs/man/doc/statalign.1">man statalign</a></td></tr>      	<tr><td><A HREF="/docs/man/doc/arcs2ps.1">man arcs2ps</a></td></tr>    	</table>  	<p>  	<dt>	<a name=STRIDE><i>stride</i> (1.0) 	<dd>	STRIDE recognizes secondary structure elements in proteins from their atomic coordinates.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>stride</td>      	<td><A HREF="/docs/man/doc/stride.1">man stride</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/stride-simple.html">stride</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/stride/stride.doc">/local/gensoft/doc/stride/stride.doc</a></td></tr>    	</table>  	<p>  	<dt>	<a name=SWISSKNIFE><i>Swissknife</i> (0.9.3) 	<dd>	an object oriented Perl library to handle  entries in SWISS-PROT format   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>  	</tr>  	<tr>  	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/Swissknife/">http://bioweb.pasteur.fr/docs/Swissknife/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=SYD><i>SYD</i>  	<dd>	Simulation d'un pedigree sur 3 gnrations pour gnrer des donnes utilisables dans les programmes de cartographie.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>syd</td>      	<td><A HREF="/docs/man/doc/syd.1">man syd</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/syd/Doc/">/local/gensoft/doc/syd/Doc</a></td></tr>    	</table>  	<p>  	<dt>	<a name=T_COFFEE><i>t_coffee</i> (1.37) 	<dd>	Multiple Sequence Alignment Combination   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>t_coffee</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/t_coffee/">/local/gensoft/doc/t_coffee</a></td></tr>      	<tr><td><A HREF="/docs/t_coffee/">http://bioweb.pasteur.fr/docs/t_coffee/</a></td></tr>      	<tr><td><A HREF="http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html">http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=TAAR><i>TAAR</i> (1.0) 	<dd>	Tree Alignment And Reconstruction   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>taar</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www.dcss.mcmaster.ca/~fliu/taar_download.html">http://www.dcss.mcmaster.ca/~fliu/taar_download.html</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/TAAR//">/local/gensoft/doc/TAAR/</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>Les matrices (SAMPLE_SCORES) peuvent etre recopiees depuis le repertoire /local/gensoft/lib/TAAR</td>       </tr>         </table>  	<p>  	<dt>	<a name=TACG><i>TACG</i> (2.391) 	<dd>	Recherche de sites d'enzymes de restriction dans une squence.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>tacg</td>      	<td><A HREF="/docs/man/man/tacg.1.html">man tacg</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/tacg.html">TACG</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/tacg/tacg2.main.html">http://bioweb.pasteur.fr/docs/tacg/tacg2.main.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=TBOB><i>TBOB</i> (6.3-p1) 	<dd>	(Text based Blast Output Browser) Affichage des rsultats de Blast.   Voir aussi : <a href="gensoft-algt.html#BOB">BOB</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>tbob</td>      	<td><A HREF="/docs/man/man/tbob.1.html">man tbob</a></td>    	</tr>  	</table>  	<p>  	<dt>	<a name=TEXSHADE><i>texshade</i> (1.5) 	<dd>	A LaTeX package for setting nucleotide and peptide alignments  Voir aussi : <a href="gensoft-algt.html#BOXSHADE">BOXSHADE</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>  	</tr>  	<tr>  	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://homepages.uni-tuebingen.de/beitz/txe.html">http://homepages.uni-tuebingen.de/beitz/txe.html</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/texshade/">/local/gensoft/doc/texshade</a></td></tr>    	</table>  	<p>  	<dt>	<a name=TIPDATE><i>TipDate</i> (1.2) 	<dd>	A program to estimate the rate of molecular  evolution and time-scale of a phylogeny from  dated sequences.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>tipdate</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>tipdate -h</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/tipdate.html">TipDate</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/TipDate//">/local/gensoft/doc/TipDate/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=TOPPRED><i>toppred</i> (1.0) 	<dd>	Topology prediction of membrane proteins   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>toppred</td>      	<td><A HREF="/docs/man/man/toppred.1.html">man toppred</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/toppred.html">toppred</a></td></tr>    	</table>  	<p>  	<dt>	<a name=TOPS><i>TOPS</i> (1.0) 	<dd>	(Protein Topology Cartoon Generation Package) Rsum graphique en 2 dimensions d'une structure.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>Tops</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/tops/tops.ps">/local/gensoft/doc/tops/tops.ps</a></td></tr>    	</table>  	<p>  	<dt>	<a name=TRANSLATE><i>TRANSLATE</i>  	<dd>	Traduction d'ADN.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>translate</td>      	<td><A HREF="/docs/man/man/translate.1.html">man translate</a></td>    	</tr>  	</table>  	<p>  	<dt>	<a name=TREEALIGN><i>treealign</i>  	<dd>	A multiple sequence alignment program that builds trees as it aligns DNA or protein sequences. It uses a combination of distance matrix and approximate parsimony methods.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>treealign</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/treealign-simple.html">treealign</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/treealign/README">/local/gensoft/doc/treealign/README</a></td></tr>      	<tr><td><A HREF="http://evolution.genetics.washington.edu/phylip/software.etc1.html#TreeAlign">http://evolution.genetics.washington.edu/phylip/software.etc1.html#TreeAlign</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/treealign//">/local/gensoft/doc/treealign/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=TREETOOL><i>TREETOOL</i> (2.0.2) 	<dd>	dition d'arbres phylogntiques.[X11]   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>treetool</td>      	<td>man treetool</td>    	</tr>  	</table>  	<p>  	<dt>	<a name=TRNASCANSE><i>tRNAscan-SE</i> (1.23) 	<dd>	Dtection d'ARN de transfert dans une squence gnomique. Trois mthodes sont combines pour affiner la recherche : cove, tRNAscan et EufindtRNA.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>tRNAscan-SE</td>      	<td><A HREF="/docs/man/man/tRNAscan-SE.1.html">man tRNAscan-SE</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/trnascan-simple.html">tRNAscan-SE</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/tRNAscan-SE//">/local/gensoft/doc/tRNAscan-SE/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=VHMPT><i>VHMPT</i> (1) 	<dd>	Viewer and editor for Helical Membrane Protein Topologies   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>vhmpt</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/VHMPT/">/local/gensoft/doc/VHMPT</a></td></tr>      	<tr><td><A HREF="http://ibms.sinica.edu.tw/~mjhwang/vhmpt/">http://ibms.sinica.edu.tw/~mjhwang/vhmpt/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=VIENNARNA><i>ViennaRNA</i> (1.4) 	<dd>	Vienna RNA package. Secondary structure prediction  and comparaison. Inverse folding, melting temperature  and energy calculation. RNAlib: library of functions for programmers.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>RNAfold</td>      	<td><A HREF="/docs/man/man/RNAfold.1.html">man RNAfold</a></td>    	</tr>  	<tr>    	<td>RNAeval</td>      	<td><A HREF="/docs/man/man/RNAeval.1.html">man RNAeval</a></td>    	</tr>  	<tr>    	<td>RNAheat</td>      	<td><A HREF="/docs/man/man/RNAheat.1.html">man RNAheat</a></td>    	</tr>  	<tr>    	<td>RNAinverse</td>      	<td><A HREF="/docs/man/man/RNAinverse.1.html">man RNAinverse</a></td>    	</tr>  	<tr>    	<td>RNAdistance</td>      	<td><A HREF="/docs/man/man/RNAdistance.1.html">man RNAdistance</a></td>    	</tr>  	<tr>    	<td>RNApdist</td>      	<td><A HREF="/docs/man/man/RNApdist.1.html">man RNApdist</a></td>    	</tr>  	<tr>    	<td>AnalyseDists</td>      	<td><A HREF="/docs/man/man/AnalyseDists.1.html">man AnalyseDists</a></td>    	</tr>  	<tr>    	<td>AnalyseSeqs</td>      	<td><A HREF="/docs/man/man/AnalyseSeqs.1.html">man AnalyseSeqs</a></td>    	</tr>  	<tr>    	<td>RNAsubopt</td>      	<td><A HREF="/docs/man/man/RNAsubopt.1.html">man RNAsubopt</a></td>    	</tr>  	<tr>    	<td>popt</td>    	</tr>  	<tr>    	<td>RNAplot</td>    	</tr>  	<tr>    	<td>b2ct</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Aide en ligne Unix complmentaire</i></td>   	</tr>    	<tr><td>man ViennaRNA</td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/rna/">ViennaRNA</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/ViennaRNA/">/local/gensoft/doc/ViennaRNA</a></td></tr>      	<tr><td><A HREF="http://www.ks.uiuc.edu/~ivo/RNA/">http://www.ks.uiuc.edu/~ivo/RNA/</a></td></tr>      	<tr><td><A HREF="/docs/ViennaRNA/RNAlib.html">http://bioweb.pasteur.fr/docs/ViennaRNA/RNAlib.html</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>  	<td><i>Remarques</i></td>  	</tr>          <tr>  	<td>See /local/gensoft/include/ViennaRNA for header files (Vienna package library users only). See /local/gensoft/doc/ViennaRNA/Perl for an example of the perl RNA module use.</td>       </tr>         </table>  	<p>  	<dt>	<a name=VITESSE><i>VITESSE</i> (1.0) 	<dd>	Calcul de pedigrees par maximum de vraisemblance.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>vitesse</td>      	<td><A HREF="/docs/man/doc/vitesse.1">man vitesse</a></td>    	</tr>  	</table>  	<p>  	<dt>	<a name=VMD><i>vmd</i> (1.2b2) 	<dd>	Visual Molecular Dynamics   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>vmd</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/vmd/vmd_help.html">/local/gensoft/doc/vmd/vmd_help.html</a></td></tr>    	</table>  	<p>  	<dt>	<a name=WEIGHBOR><i>Weighbor</i> (1.2.1) 	<dd>	Weighted neighbor joining.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>weighbor</td>      	<td><A HREF="/docs/man/man/weighbor.1.html">man weighbor</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/weighbor.html">Weighbor</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www.t10.lanl.gov/billb/weighbor/">http://www.t10.lanl.gov/billb/weighbor/</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/Weighbor//">/local/gensoft/doc/Weighbor/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=WHATIF><i>whatif</i> (19991018-1516) 	<dd>	Un programme pour la manipulation, l'analysis,  et la visualation de proteins[X11]   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>    	</tr>  	<tr>    	<td>whatif</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="http://swift.EMBL-Heidelberg.DE/whatif">whatif</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td>/local/gensoft/lib/whatif99/writeup</td></tr>    	</table>  	<p>  	<dt>	<a name=WISE2><i>WISE2</i> (2.2.0) 	<dd>	Comparaison de squences d'ADN  contre des squences ou des profils de protines. Mthode robuste par rapport aux erreurs dans les  squences d'ADN.  Voir aussi : <a href="#HMMER">HMMER</a>, <a href="#MSPCRUNCH">MSPCRUNCH</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>dba</td>      	<td><A HREF="/docs/man/doc/dba.1">man dba</a></td>    	</tr>  	<tr>    	<td>dnal</td>      	<td><A HREF="/docs/man/doc/dnal.1">man dnal</a></td>    	</tr>  	<tr>    	<td>estwise</td>      	<td><A HREF="/docs/man/doc/estwise.1">man estwise</a></td>    	</tr>  	<tr>    	<td>estwisedb</td>      	<td><A HREF="/docs/man/doc/estwisedb.1">man estwisedb</a></td>    	</tr>  	<tr>    	<td>genewise</td>      	<td><A HREF="/docs/man/doc/genewise.1">man genewise</a></td>    	</tr>  	<tr>    	<td>genewisedb</td>      	<td><A HREF="/docs/man/doc/genewisedb.1">man genewisedb</a></td>    	</tr>  	<tr>    	<td>genomewise</td>      	<td><A HREF="/docs/man/doc/genomewise.1">man genomewise</a></td>    	</tr>  	<tr>    	<td>psw</td>      	<td><A HREF="/docs/man/doc/psw.1">man psw</a></td>    	</tr>  	<tr>    	<td>pswdb</td>      	<td><A HREF="/docs/man/doc/pswdb.1">man pswdb</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://www.sanger.ac.uk/Software/Wise2/">http://www.sanger.ac.uk/Software/Wise2/</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/wise2//">/local/gensoft/doc/wise2/</a></td></tr>    	</table>  	<p>  	<dt>	<a name=XBLAST><i>XBLAST</i>  	<dd>	Masquage des rsultats de Blast.    	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>xblast</td>      	<td><A HREF="/docs/man/man/xblast.1.html">man xblast</a></td>    	</tr>  	</table>  	<p>  	<dt>	<a name=XGRAIL><i>XGRAIL</i> (1.3c) 	<dd>	Recherche de rgions codantes, modles de gnes, traductions, sites fonctionnels, rptitions. [X11]  Voir aussi : <a href="gensoft-na.html#GRAILCLNT">GRAILCLNT</a>, <a href="#NETGRAIL">NETGRAIL</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>xgrail</td>      	<td><A HREF="/docs/man/doc/xgrail.1">man xgrail</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/xgrail/grail.publ">/local/gensoft/doc/xgrail/grail.publ</a></td></tr>      	<tr><td><A HREF="/docs/doc-gensoft/xgrail/orgseqs//">/local/gensoft/doc/xgrail/orgseqs/</a></td></tr>      	<tr><td><A HREF="http://grail.lsd.ornl.gov/manuals/grail1.3-genquest.9605.shtml">http://grail.lsd.ornl.gov/manuals/grail1.3-genquest.9605.shtml</a></td></tr>    	</table>  	<p>  	<dt>	<a name=XMMOL><i>XmMol</i> (3.1) 	<dd>	Visualisation en modlisation molculaire.[X11]   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>XmMol</td>      	<td><A HREF="/docs/man/doc/XmMol.1">man XmMol</a></td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="http://condor.urbb.jussieu.fr/XmMol.php">http://condor.urbb.jussieu.fr/XmMol.php</a></td></tr>    	</table>  	<p>  	<dt>	<a name=XNU><i>XNU</i>  	<dd>	Masque les rptitions en tandem dans une squence.   Voir aussi : <a href="gensoft-tools.html#SEG">Seg</a>.   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>xnu</td>      	<td><A HREF="/docs/man/man/xnu.1.html">man xnu</a></td>    	</tr>  	</table>  	<p>  	<dt>	<a name=XPOUND><i>xpound</i> (01/95) 	<dd>	Probabilistic model for detecting coding regions in DNA sequences   	<table border=1 cellpadding=3 cellspacing=1 width=80%>  	<tr>    	<td><i>Commandes Unix</i></td>      	<td><i>Aide en ligne Unix</i></td>    	</tr>  	<tr>    	<td>xpound</td>      	<td><A HREF="/docs/man/doc/xpound.1">man xpound</a></td>    	</tr>  	<tr>    	<td>xreport</td>    	</tr>  	<tr>    	<td>xpscript</td>    	</tr>  	<tr>    	<td>xtrain</td>    	</tr>  	<tr>    	<td>xspec</td>    	</tr>  	<tr>    	<td>xshow</td>    	</tr>  	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Serveur</i></td>   	</tr>    	<tr><td><A HREF="/seqanal/interfaces/xpound-simple.html">xpound</a></td></tr>    	</table>  	<table border=1 cellpadding=3 cellspacing=1 width=80%> 	<tr>   	<td><i>Documents</i></td>   	</tr>    	<tr><td><A HREF="/docs/doc-gensoft/xpound//">/local/gensoft/doc/xpound/</a></td></tr>    	</table>  	<p>  </dl> <p>  </ul>  </BODY> </HTML> 
