phangorn: phylogenetic analysis in R

TLDR

phangorn is a package for phylogenetic reconstruction and analysis in the R language. The package extends the general ML framework to estimate mixture and partition models and provides functions for comparing trees, models, splits, simulating data, and performing congruence analyses. Previously it was only possible to estimate phylogenetic trees with distance methods in R; phangorn now offers reconstruction with distance-based methods, maximum parsimony, or maximum likelihood and performing Hadamard conjugation. phangorn is available on CRAN (http://cran.r-project.org/web/packages/phangorn/index.html), licensed under GPL 2, with contact at [e-mail] and supplementary data at Bioinformatics online.

Abstract

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. Contact: [e-mail] Supplementary information: Supplementary data are available at Bioinformatics online.