Joe Felsenstein's suite of programs implementing perhaps the widest range of phylogenetic inference package. The most widely distributed phylogeny software. Includes distance, likelihood and parsimony methods for a wide range of different types of data, and runs on most platforms.

Open source software for estimation of phylogenies using Bayesian inference.

A brief overview of using NONA for phylogenetic analysis.

Phylogenetic analyses of DNA or protein sequences using maximum likelihood.

Graphical color interface for molecular phylogenetic inference. It performs neighbor-joining, parsimony, and maximum likelihood methods and bootstrap with any of them.

Computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood.