phangorn: phylogenetic analysis in R

Research output: Contribution to journalArticleResearchpeer-review

Abstract

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 http://cran.r-project.org/web/packages/phangorn/index.html. phangorn is licensed under GPL 2.

Original languageEnglish
Pages (from-to)592-3
Number of pages2
JournalBioinformatics
Volume27
Issue number4
DOIs
Publication statusPublished - 15 Feb 2011
Externally publishedYes

Keywords

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

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