From Bioinformatics.Org Wiki
- ATV - a phylogenetic tree display tool
- Clann - software for investigating phylogenomic information using supertrees
- fastDNAml - Estimates maximum likelihood phylogenetic trees from nucleotide sequences
- Friend - an integrated front-end application for bioinformatics
- 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 - performs molecular phylogenetic inference using maximum likelihood and Bayesian (MCMC) techniques
- 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
- 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.
- T-REX - Webserver for tree inference (RAxML, PhyML, NINJA) and visualization, horizontal gene transfer detection (HGT-detection), and multiple sequence alignment (Muscle, MAFFT and ClustalW).
Phylogenetic tree reconstruction