PHYBASE provides functions to read, write, manipulate, simulate, estimate, and summarize phylogenetic trees (gene trees and species trees). The major features of Phybase include: • Simulate DNA sequences from Species trees • 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) • Estimate species trees using STAR/STEAC (Liu et al 2009a and 2009b), and MT (maximum tree) (Liu et al 2009c). • Model selection and validation for phylogenetic models Phybase2.0 is now available at Github and manual 1. To install phybase from Github, type install_github("lliu1871/phybase") in R, or download the package and install it locally. 2. The functions in phybase2.0 are renamed to form clusters - "alignment", "file", "simulation", etc. The newly proposed hypothesis tests for species trees and gene trees are added in the package. The functions for trimming and cleaning alignments are added in the package. Old versions 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
