Package: phybase
Type: Package
Title: Basic functions for phylogenetic analysis
Version: 1.1
Date: 2008-03-25
Author: Liang Liu
Maintainer: Liang Liu <lliu@oeb.harvard.edu>
Depends: Matrix, ape
Description: This package provides functions to read, write,
        manipulate, estimate, and summarize phylogenetic trees
        including species trees which contain not only the topology and
        branch lengths but also population sizes. The input/output
        functions can read tree files in which trees are presented in
        parenthetic 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. Some basic functions have already been established in
        the package for manipulating trees such as deleting and
        swapping nodes, rooting and unrooting trees, changing the root
        of the tree. The package also includes functions such as
        "consensus", "coaltime, "popsize", "treedist" for summarizing
        phylogenetic trees, calculating the coalescence time,
        population size, and tree distance. The function maxtree is
        built in the package to esimtate the species tree from multiple
        gene trees.
License: GPL (>= 2)
Packaged: 2012-10-29 08:59:26 UTC; ripley
Repository: CRAN
Date/Publication: 2012-10-29 08:59:26
