Phybase

PHYBASE provides functions to read, write, manipulate, simulate, estimate, and summarize phylogenetic trees (gene trees and species trees). The major features of Phybase include:

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

phybase_1.5.tar.gz (R > 3.0)               Manual      note: phybase1.5 has fixed a bug in star.sptree, The previous version of star.sptree works well for single-allele data, but may not correctly calculate the distance matrix when the input data contain multiple alleles and missing taxa for some genes. 

phybase_1.4.tar.gz (R > 3.0)               Manual

phybase_1.3.tar.gz (R 2.14 and 2.15)   Manual

phybase_1.2.tar.gz (R 2.14 and 2.15)   Manual