SOFTWARE

IMPORTANT NEWS: Several old programs have been discontinued and will not be maintained or supported anymore.
  • jMODELTEST 2 (NEW!): is a program for model selection a model averaged phylogeny estimation that uses Phyml. It implements different strategies, like hLRTs, dLRTs, AIC, BIC and the DT methods.jModelTest 2 includes High Performance Computing (HPC) capabilities and additional features like new strategies for tree optimization, model-averaged phylogenetic trees (both topology and branch lenght), heuristic filtering and automatic logging of user activity.

  • PROTTEST 3: High Performance Computing selection of models of protein evolution. Link to the prottest 2 server.

  • ALTER: a program-oriented alignment format converter. Very useful to work with different phylogenetic programs

  • NETRECODON simulates coding sequences with intracodon recombination, migration and growth.

  • NETTEST WEB SERVER: This server allows the characterization of explicit networks. Current version is 1.0.

  • GEODIS implements the nested clade phylogeographic analysis (NCPA) of the geographical distribution of haplotypes developed by Alan Templeton et al. This methodology aims to separate population processes from population patterns. Current version is 2.6 (28 April 2009)

  • GENDECODER is a web server to help characterizing the genetic code of metazoan mitochondrial genomes. Current version is 1.6 (4 January 2007).

  • TREESCAN provides p-values for the test of genotype/phenotype association between evolutionary clades and continuous traits, using haplotype trees. Current version is 1.0 (19 July 2006).

  • TCS estimates phylogenetics networks from DNA sequences or nucleotide distances using the statistical parsimony algorithm (Templeton et al. 1992, Genetics 132:619-633). TCS also estimates the 95% parsimony limits and outgroup weights. This version maps changes along branches. Current version is 1.21.

  • MITOBANK is a program for the retrieval and gene-parsing of mitochondrial genomes. Current version is 2.1.

Correspondence about the programs above should be addressed to David Posada at

  • RDP is a Windows program developed by Darren Martin for the detection of recombination from DNA alignments. It includes several methods, like RDP, MaxChi, Chimaera, Geneconv, Bootscan and Siscan. Current version is Beta 0.8



This document last modified Tuesday March 19, 2013