DendroPy: a Python library for phylogenetic computing

Bioinformatics. 2010 Jun 15;26(12):1569-71. doi: 10.1093/bioinformatics/btq228. Epub 2010 Apr 25.


DendroPy is a cross-platform library for the Python programming language that provides for object-oriented reading, writing, simulation and manipulation of phylogenetic data, with an emphasis on phylogenetic tree operations. DendroPy uses a splits-hash mapping to perform rapid calculations of tree distances, similarities and shape under various metrics. It contains rich simulation routines to generate trees under a number of different phylogenetic and coalescent models. DendroPy's data simulation and manipulation facilities, in conjunction with its support of a broad range of phylogenetic data formats (NEXUS, Newick, PHYLIP, FASTA, NeXML, etc.), allow it to serve a useful role in various phyloinformatics and phylogeographic pipelines.

Availability: The stable release of the library is available for download and automated installation through the Python Package Index site (, while the active development source code repository is available to the public from GitHub (

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms
  • Computational Biology / methods*
  • Databases, Factual
  • Phylogeny*
  • Programming Languages
  • Software*