phyloch-package: Phylogenetic Data Analysis And Display
In fmichonneau/phyloch: Tools for phylogenetics and taxonomy

Description Details Author(s) See Also

This package is intended as a (modest) companion to the great ape package, which it extends in two dimensions. First, it provides a series of wrappers for commonly used software packages and second, it contains some more tools for plotting of phylogentic trees.

Package:	phyloch
Type:	Package
Version:	1.5-5
Date:	2013-09-04
License:	GPL (>= 2)

There are several functions for reading and writing DNA sequences in FASTA, PHYLIP, and NEXUS format: read.fas, read.phy, read.nex, write.fas, write.phy, write.nex, and write.partitioned.nex. Several functions are provided to extend the capabilities of plot.phylo from the ape package. Use clade.bars and box.clades to summarize clades and provide labels for clades in a phylogeny. tip.color and edge.color can be used in a simple way in conjunction with plot.phylo to create different color patterns for tips and edges. Some functions are available for integrating BEAST with R. XML input files for BEAST can be generated with rbeauti. Two functions are designed to read TreeAnnotator output: read.beast will render an object of class phylo with additional node statistics appended as list elements. These additional node statistics will be lost be the subsequent use of ladderize or rotate (or similar functions that change the ordering of internal nodes); in this case node.trans can be used to reappend the nodestatistics.read.beast.table also parses the TreeAnnotator output, but returns a matrix of node statistics. Finally, HPD intervals can be plotted using HPDbars. This package itself does not implement techniques for phylogenetic analyses, but provides a series of wrappers for commonly used software packages. Sequence alignment can be done with the mafft and prank; cleaning of sequences with gblocks and aliscore. The function raxml and mrbayes are intended for phylogentic tree search. Running mrbayes with argument run = FALSE can be used to create MrBayes-executable NEXUS files. Finally, wrappers is provided for Multistate in the BayesTraits package (see multistateML and multistateMCMC).