- Phylogeny Programs
- The most complete list of phylogeny softwares
(Felsenstein).
- PHYLIP
- 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.
- PHYML
- 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.
- PAML
- Phylogenetic Analysis by Maximum Likelihood (Ziheng Yang).
- Seq-Gen
- An application for the Monte Carlo simulation of DNA and amino acid sequence evolution along
phylogenetic trees (Andrew Rambaut and Nick Grassly).
