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.
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.
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.