资 源 简 介
PHYBASE provides functions to read, write, manipulate, simulate, estimate, and summarize phylogenetic trees (gene trees and species trees). The input/output functions can read and write phylogenetic trees in the Nexus and Phylip format. The trees are read in as a string and then transformed to a matrix which describes the relationship of nodes and branch lengths. The nodes matrix provides an easy access for developers to further manipulate the tree, while the tree string provides interface with other phylogenetic R packages such as "ape". The input/output functions can also be used to change the format of tree files between Nexus and Phylip. Basic functions are available in the package for manipulating phylogenetic trees such as deleting and swapping nodes, rooting and unrooting trees, changing the root of the tree. The package also includes functions such as "consense", "coaltime, "popsize", "treedist" for summarizing phylogenetic trees.
