Inference of phylogenetic trees using Distance, Maximum Likelihood, Maximum Parsimony, Bayesian methods and related workflows.Į. Workflow platform dedicated to phylogenetic and general bioinformatic analysis Methods for estimating phylogenies include neighbor-joining, maximum parsimony (also simply referred to as parsimony), UPGMA, Bayesian phylogenetic inference, maximum likelihood and distance matrix methods. Such tools are commonly used in comparative genomics, cladistics, and bioinformatics. This list of phylogenetics software is a compilation of computational phylogenetics software used to produce phylogenetic trees.