phybase

Phybase provides functions to read, write, manipulate, simulate, estimate, and summarize phylogenetic trees (gene trees and species trees).

1. Read and write sequences in Nexus and Phylip format.
2. Read and write trees in Nexus and Phylip format.
3. Summarize trees.
4. Simulate DNA sequences from gene trees
5. Simulate gene trees from a species tree under the multispecies coalescent model.
6. Single locus and multilocus bootstrapping (Seo 2008).
7. Calculate the probability density function of a set of gene trees given a species tree. (Rannala and Yang 2003)
8. Manipulate trees.
9. Estimate species trees using STAR/STEAC (Liu et al 2009a and 2009b), and MT (maximum tree) (Liu et al 2009c).
10. Model selection and validation of the substitution models.

Citation: Liu, L., and L. Yu. Phybase: an R package for species tree analysis. Bioinformatics. 2010 26(7):962-963.

Old versions are available at https://github.com/lliu1871/oldversion