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

phangorn: phylogenetic analysis in R.

Author information

1
UMR CNRS 7138 Systématique, Adaptation, Evolution, Université Pierre et Marie Curie, Muséum National d'Histoire Naturelle, Paris, France. klaus.kschliep@snv.jussieu.fr

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.

PMID:
21169378
PMCID:
PMC3035803
DOI:
10.1093/bioinformatics/btq706
[Indexed for MEDLINE]
Free PMC Article
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