Softwares and data sets

• MPC, a method to build a set of consensus trees instead of a single one.
  
  
• ATGC, bioinformatics platform of LIRMM.
  
  
• PERMUTMATRIX, a graphical software for analyzing and visualizing gene expression data.
  
  
• PHYML, fast and accurate phylogenetic reconstruction by maximum likelihood ; plus numerous test sets.
  
  
• FastME, very fast and yet accurate distance-based phylogenetic reconstruction.
  
  
• DTscore, a distance based algorithm to reconstruct the duplication history of tandemly repeated sequences.
  
  
• GAMMA, a distance based phylogeny inference program to deal with varying across sites substitution rates.
  
  
• Q*, a quartet based method that infers reliable trees.
  
  
• BIONJ, an improved version of NJ based on a model of sequence data.
  
  
• QR2, a reduction algorithm for approximating a (nonmetric) dissimilarity by a tree distance.
  
  
• Model Trees, 48000 data sets built from 12-taxon model trees, to test phylogeny methods.
  
  
• 5000 data sets from random 24-taxon trees et 2000 data sets from 96-taxon random trees, to test phylogeny methods.
  
  
• 10000 data sets with 100-taxon trees evolving under a gamma or covarion model.