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.
|License:||GPL (>= 2)|
There are several functions for reading and writing DNA sequences in FASTA, PHYLIP, and NEXUS format:
Several functions are provided to extend the capabilities of
plot.phylo from the ape package. Use
box.clades to summarize clades and provide labels for clades in a phylogeny.
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
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
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
prank; cleaning of sequences with
aliscore. The function
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
Natalie Cusimano, Christoph Heibl Maintainer: Christoph Heibl (email@example.com)
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