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Phylogeny Programs
Owing to other pressures on my time, I cannot devote much time to searching for new programs, so their authors are begged to (please!)
Phylogenetic Analysis by Maximum Likelihood (PAML)
PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed for academic use free of charge by Ziheng Yang.MEGA - Molecular Evolutionary Genetics Analysis
MEGA is an integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, inferring ancestral sequences, and testing evolutionary hypotheses.
HyPhy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. It features a complete graphical user interface (GUI) and a rich scripting language for limitless customization of analyses.
start [HyPhy]
Phylo_win has now been replaced by SeaView version 4 that performs both multiple sequence alignment (with muscle or clustalw2) and phylogenetic tree building (by parsimony, distances or maximum likelihood) for DNA or protein sequences. Reference :
Phylo_win
NJplot
NJplot is a tree drawing program able to draw any phylogenetic tree expressed in the Newick phylogenetic tree format ( e.g. , the format used by the PHYLIP package).
MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters. An abundance of evolutionary models, including 4 X 4, doublet, and codon models for nucleotide data and many of the standard rate matrices for amino acid data;