SOFTWARE -> Frequently Asked Questions (FAQ) about these programs NETRECODON updated! simulates coding sequences with intracodon recombination, migration and growth. Current version is 5.0.6 (02 November 2009). RECODON updated! simulates coding sequences with inter-codon recombination, migration and growth. Current version is 1.6.0 (25 November 2009). PROTTEST updated! estimates the empirical model of aminoacid substitution that fits the data best among 112 candidate models. PROTTEST calculates AIC, AICc and BIC values, and obtain a rank of model fits, model-averaged parameter estimates, or measures of parameter importance. Current version is 2.4 (1 October 2009). GEODIS updated! 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) jMODELTEST is a new program for model selection a model averaged phylogeny estimation that uses Phyml. It implements several hLRTs, dLRTs, AIC, BIC and the DT methods. Current version is 1.0.1 (10 April 2008). 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). MODELTEST WEB SERVER This server offers online the calculations implemented in Modeltest. Current version is 1.0. 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. MODELTEST selects the model of DNA substitution that fits the data best among 56 models. This version implements the hLRT, AIC and BIC frameworks. It also calculates model averaged estimates and parameter importance. Current version is 3.7. MITOBANK is a program for the retrieval and gene-parsing of mitochondrial genomes. Current version is 2.1. SNPSIM is a program for the simulation of samples of SNPs and haplotypes under the coalescent with hotspot recombination, implementing several demographics and mutation models. Current version is 0.8. COLLAPSE is a tool for collapsing sequences to haplotypes. Current version is 1.2.

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 KPAIRWISE is an extension implemented by Antonio Carvajal-Rodríguez of the program LDhat (Gil McVean's) for the estimation of the population recombination rate under complex models. Current version is 0.2.

This document last modified Friday November 20, 2009