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Motivation: Phybase is an R package for phylogenetic analysis using species trees. It provides functions to read, write, manipulate, simulate, estimate, summarize and plot species trees, which contain not only the topology and branch lengths but also population sizes.

Availability: The Phybase package is available at the R repository. The manual and supporting materials including source code, sample R code and sample data files for the species tree analysis are available at http://stat.osu.edu/∼liuliang/research/phybase.html

Contact:  [email protected]