MPC is a method to build consensus trees, which builds a group of trees instead of a single one. It aims at displaying all the splits appearing in more than a pre-defined proportion of the input trees in a minimum number of consensus trees, or poles. The problem is equivalent to a graph colouring problem (Cécile Bonnard, Vincent Berry and Nicolas Lartillot, 2006, Systematic Biology, in press).
User's Guide
You can mainly set three parameters: (n) to fix the number of poles in the MPC, (alpha) a threshold to discard the less frequent splits, and (beta) a threshold of split co-occurences in the input trees. See details below.
You can use any combination of the following parameters.
Allows you to specify the mimimum weight that splits should have in order to be displayed in the MPC. The weight of a split is defined as the proportion of the trees of the input collection in which it appears.
-n <number of poles>:
Allows you to specify the number of poles that you want in the output. The alpha threshold will then be tuned accordingly (i.e. the program will choose the lowest value of alpha allowing the specified number of poles). For 3 or more trees, a heuristic method is used, and an exact one in the 2-pole case.
-beta <co-occurence threshold> :
If you want to display in the same tree only splits which appear together in more than the specified proportion of the trees.
-m <max> :
Sometimes, MPC will stop because the maximum number of poles is reached (10 by default). Use this option if you want to allow more than 10 trees, in the MPC.
-ps :
If you want the output in the post-script format.
-o <outfile> :
allows you to specify the base name of the output. By default,
outfile = infile. This name is then combined with various
extensions, depending on the exact output.
Input files
MPC takes as entry a tree collection in nexus format.
Output files
There are three types of output files : split list, tree list (phylip format) and tree list in ps format.
Output files are named as follow :
*.b : initial split list
*.K : Kernel split list
*.K_tree : Kernel tree (phylip format)
*.K_tree.ps : Kernel tree (ps format)
*.MPC : MPC split list
*.MPC_tree : MPC trees (phylip format)
*.MPC_tree.ps : MPC trees (ps format)
outfile.20.* : if you used a threshold of 20 %.
outfile.n2.* : if you wanted only two poles in the MPC.
*.c20* : if you use the "compatibility option" with a threshold of 20 %.
Download
Linux
Executable (2.5 Mo) : stable : in static (using STL version 4.6.2-2 and ubuntu 5.04). Dont forget to keep header.tex because it's used to build ps files.
Mac OS X
Executable (2 Mo) : stable : in static. Dont forget to keep header.tex because it's used to build ps files.
Windows
Executable (2 Mo) : stable : in static. Dont forget to keep header.tex because it's used to build ps files. (Windows XP Professionel, version 2002, SP2)
