Phylogeny Programs
The most complete list of phylogeny softwares (Felsenstein).
PHYlogeny Inference Package (Felsenstein), the most complete free package for various phylogenetic studies. The only competitor is PAUP*, an all-purpose commercial package which, however, will not be introduced here.
Simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood (Stephane Guindon and Olivier Gascuel). PHYML is almost the only hope to build a tree containing hundreds of sequences with likelihood methods. Most of other softwares will take irrealistic long time to achieve such a goal. PHYML's paper is described as a fast breaking paper. It has been cited over 400 times. An enhanced version of PHYML is widely used by Ensembl Compara and TreeFam.
Phylogenetic Analysis by Maximum Likelihood (Ziheng Yang).
An application for the Monte Carlo simulation of DNA and amino acid sequence evolution along phylogenetic trees (Andrew Rambaut and Nick Grassly).