phangorn: phylogenetic analysis in R

Bioinformatics. 2011 Feb 15;27(4):592-3. doi: 10.1093/bioinformatics/btq706. Epub 2010 Dec 17.


Summary: phangorn is a package for phylogenetic reconstruction and analysis in the R language. Previously it was only possible to estimate phylogenetic trees with distance methods in R. phangorn, now offers the possibility of reconstructing phylogenies with distance based methods, maximum parsimony or maximum likelihood (ML) and performing Hadamard conjugation. Extending the general ML framework, this package provides the possibility of estimating mixture and partition models. Furthermore, phangorn offers several functions for comparing trees, phylogenetic models or splits, simulating character data and performing congruence analyses.

Availability: phangorn can be obtained through the CRAN homepage phangorn is licensed under GPL 2.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / methods*
  • Likelihood Functions
  • Models, Genetic*
  • Phylogeny*
  • Software*