From Bioinformatics.Org Wiki
- ATV - a phylogenetic tree display tool
- Clann - Clann: Software for investigating phylogenomic information using supertrees. This implements several methods of Supertree analysis (which are used as optimality criteria) and allows exhaustive and heuristic searches of tree-space to find the best supert
- fastDNAml - Estimates maximum likelihood phylogenetic trees from nucleotide sequences
- Friend - Friend, an Integrated Front-end Application for Bioinformatics
- MOLPHY - A Computer Program Package for Molecular Phylogenetics including ProtML
- njplot - NJplot is a tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format
- PAML - Phylogenetic Analysis by Maximum Likelihood
- Paup - Software package for inference of evolutionary trees
- PHASE - PHASE performs molecular phylogenetic inference using maximum likelihood and Bayesian (MCMC) techniques. Specific RNA substitution models are implemented to account for the correlated mutations of paired bases in RNA helices.
- PHYLIP - PHYLIP is a free package of programs for inferring phylogenies.
- PhyloDraw - PhyloDraw is a drawing tool for creating phylogenetic trees. PhyloDraw supports various kinds of multialignment programs (Dialign2, Clustal-W, Phylip format, and pairwise distance matrix) and visualizes various kinds of tree diagrams, e.g. rectangular cl
- PhyloGrapher - PhyloGrapher is a program designed to visualize and study evolutional relationship between families of homologous genes or proteins. PhyloGrapher is a drawing tool that generates custom graphs out of the given set of genes based on distance matrix file.
- phylowin - Phylo_win is a graphical colour interface for molecular phylogenetic inference.
- PyPhy - PyPhy is a set of python scripts and modules for automatic, large-scale reconstructions of phylogenetic relationships of complete microbial genomes.
- unrooted - Unrooted is a tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format in an unrooted way, that is, using a circular shape, with labels aligned with terminal branches.
- UGENE - has a graphical user friendly interface for PHYLIP package.