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Phylogenetics is generally the process of building trees representing the evolutionary history of a set of taxa based on characters. See also Cladistics.

Molecular evolution tools are also supported by BioPerl although they fall under the Phylo namespace.


Phylogenetic support

NEXUS multiple alignment format for use with PAUP, MrBayes and other tools is supported through Bio::AlignIO and Bio::TreeIO which respectively parse alignment and tree data in NEXUS format. There is some interest in a project to better support NEXUS format in BioPerl which will hopefully build on work like Nexplorer [1].

PHYLIP is also supported through Run package to automate running of the tools as well as parsing the PHYLIP multiple alignment format. Distance matrices can be parsed with Bio::Matrix::IO.

Parsing Trees

Trees can be parsed with the Bio::TreeIO. The Tree HOWTOs provide some help with this.

Building Trees

UPGMA and NJ Trees can be built natively (in Perl) with Bio::Tree::DistanceFactory. Several external tools for constructing trees are supported in the Run package.

Related Projects


  1. Gopalan V, Qiu WG, Chen MZ, and Stoltzfus A. Nexplorer: phylogeny-based exploration of sequence family data. Bioinformatics. 2006 Jan 1;22(1):120-1. DOI:10.1093/bioinformatics/bti747 | PubMed ID:16267087 | HubMed [nexplorer]
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