Supplementary information:Supplementary data are available at Bioinformatics online.
With more than 20 packages devoted to phylogenetics, the R software (R Development Core Team, 2009) has become a standard in phylogenetic analysis (see http://cran.r-project.org/web/views/Phylogenetics.html for an overview). However so far it was only possible to estimate phylogenetic trees with distance methods in R. The
MP is an optimality criterion for which the preferred tree is the tree that requires the least changes to explain some data. In
The ML function
For nucleotide data all models implemented in ModelTest (Posada, 2008) are available (e.g. “JC” or “GTR”). Moreover any reversible model can be specified by the user for different character states. For amino acids, the main common rate matrices are provided, e.g. WAG (Whelan and Goldman, 2001) or LG (Le and Gascuel, 2008). Additionally rate matrices can also be estimated. For instance Mathews et al., 2010 used the function
The author thanks Emmanuel Paradis, Eric Bapteste and Philippe Lopez for useful discussions and Thibaut Jombart and three anonymous referees for their comments which helped to improve the manuscript.
Funding: K.S. was supported by the Muséum National D'Histoire Naturelle.
Conflict of Interest: none declared.