phangorn

phangorn is a package for phylogenetic reconstruction and analysis in the R language. phangorn 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.

You can install

• the latest released version install.packages("phangorn")
• the latest development version devtools::install_github("KlausVigo/phangorn")

You may need to install first the Biostrings package from bioconductor

source("http://bioconductor.org/biocLite.R")
biocLite("Biostrings")

If you use phangorn please cite:

Schliep K.P. 2011. phangorn: phylogenetic analysis in R. Bioinformatics, 27(4) 592-593

License

phangorn is licensed under the GPLv2.