Phybase: Phylogenetic analysis of multilocus sequences in R

                                                 Liang Liu (lliu@oeb.harvard.edu)                                                          Lili Yu

                                      Department of Organismic and Evolutionary biology                                     Department of Biostatistics     

                                                           Harvard University                                                                     Georgia Southern University

Phybase is an R package for phylogenetic analysis of  multilocus sequences under the multi-species coalescence model. The analysis is based on the summary statistics of coalescence times among gene trees estimated from the multilocus sequence data. This package provides functions to read, write, manipulate, simulate, 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 and write phylogenetic trees in Newick 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. The major features of Phybase include:

• Read and write sequences in PHYLIP or NEXUS format.
• Read and write trees in Newick format.
• Summarize trees.
• Simulate DNA sequences from gene trees under substitution models.
• Simulate gene trees from a species tree under the multi-species model.
• Manipulate trees.
• Estimate species trees using STEAC, STAR (Liu et al 2009), and MT (maximum tree, Liu et al 2009).

• Phybase has been uploaded to the R repository.
• To install phybase, type install.packages("phybase",contriburl="http://cran.cnr.Berkeley.edu/bin/windows/contrib/2.9") in R.
• Manual and mammal.nex, treefile.t.
• Reference manual: a complete list of commands in phybase as well as examples for using these commands.
• An example of R codes (rcode_steac_star.txt) for analyzing mammal.txt using STAR and STEAC.

Download and install the package locally:

• Download Phybase (version 1.0 and version 1.1) and ape.
• Instructions (file1 and file2) for installing packages in R
• Install ape
• Install Phybase (manual)

Developers:

• Instruction for writing a package in R
• R developer
• Developer list (under construction)

Copyright 2007 by Liang Liu. The author holds no responsibility for any damage resulting from the use of this package. Please send the bug reports and suggestions to lliu@oeb.harvard.edu. You are welcome to add useful subroutines and make contributions to the package. Your name will be added on the list of contributors.