This package presents a set of functions that were formerly included in the phyloch package and which wrap popular phylogenetic software for sequence alignment, masking of sequence alignments, and estimation of phylogenies and ancestral character states.
| Package: | ips |
| Type: | Package |
| Version: | 0.0.11 |
| Date: | 2019-06-20 |
| 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, and write.nex.
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).read.beast.table also parses the TreeAnnotator output, but returns a matrix of node statistics.
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 phylogenetic 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).
Several plotting functions (HPDbars, clade.bars, box.clades, box.tips, tip.color, edge.color have been moved to the viper package.