List of phylogenetics software

This list of phylogenetics software is a compilation of computational phylogenetics software used to produce phylogenetic trees. Such tools are commonly used in comparative genomics, cladistics, and bioinformatics. Methods for estimating phylogenies include neighbor-joining, maximum parsimony (also simply referred to as parsimony), unweighted pair group method with arithmetic mean (UPGMA), Bayesian phylogenetic inference, maximum likelihood, and distance matrix methods.

• List of phylogenetic tree visualization software

• Complete list of Institut Pasteur phylogeny webservers
• ExPASy List of phylogenetics programs
• A very comprehensive list of phylogenetic tools (reconstruction, visualization, etc.)
• Another list of evolutionary genetics software
• A list of phylogenetic software provided by the Zoological Research Museum A. Koenig
• MicrobeTrace available at https://github.com/CDCgov/MicrobeTrace/wiki