NOTE:
ips
contains most functions that were formerly included in thephyloch
package plus some more recent functions. Thosephyloch
functions related to tree plotting have been moved to theviper
package.
This is a bundle of functions that present interfaces to popular phylogenetic software for sequence alignment, masking of sequence alignments, and estimation of phylogenies and ancestral character states. In additions, there functions for reading, manipulating and writing phylogenetic data (multiple sequence alignments and phylogenetic trees).
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
are 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.
ips
is available via CRAN and can be installed:
install.packages("ips")
Or you can install the development version via GitHub with:
# install.packages("devtools")
devtools::install_github("heibl/ips")