phangorn: phylogenetic analysis in R

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.

Fig. 1.

phylogenetic tree with bootstrap support on the edges for the data of Rokas et al., 2003.

Fig. 2.

Lento plot of the edge weights from sequence spectrum for the data of Rokas et al., 2003. On the x-axis the splits or edges are represented by the dots overlying the graph. The bars above the axis indicate the edge weights or the support of a split, bars below represent the conflict with this split, i.e. the sum of the edge weights which are incompatible with this split.