ips: Interfaces to Phylogenetic Software in R
Version 0.0-7

This package provides functions that wrap popular phylogenetic software for sequence alignment, masking of sequence alignments, and estimation of phylogenies and ancestral character states.

AuthorChristoph Heibl <christoph.heibl@gmx.net>
Date of publication2014-11-10 00:38:44
MaintainerChristoph Heibl <christoph.heibl@gmx.net>
LicenseGPL (>= 2)
Version0.0-7
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("ips")

Getting started

Package overview

Popular man pages

aliscore: Masking of Sequence Alignments with ALISCORE
code.simple.gaps: Simple Gap/Indel Coding
collapseUnsupportedEdges: Collapse Unsupported Edges
deleteGaps: Remove Gap/Indel Positions from Alignment
mrbayes: Bayesian MCMC Tree Search with MrBayes
pis: Number of Potentially-Informative Sites
sister: Identification of Sister Nodes and Clades
See all...

All man pages Function index File listing

Man pages

aliscore: Masking of Sequence Alignments with ALISCORE
code.simple.gaps: Simple Gap/Indel Coding
collapseUnsupportedEdges: Collapse Unsupported Edges
deleteEmptyCells: Delete Spurious Rows and Columns from DNA Alignments
deleteGaps: Remove Gap/Indel Positions from Alignment
descendants: Descendants of an Internal Node in a Phylogeny
fixNodes: Standard Node Numbering in Phylo Objects
gblocks: Masking of Sequence Alignments with GBLOCKS
ips.16S: Bark Beetle 16S Sequences
ips.28S: Bark Beetle 28S Sequences
ips.cox1: Bark Beetle COX1 Sequences
ips-internal: Internal IPS Functions
ips-package: Interfaces to Phylogenetic Software
ips.tree: Ips Phylogeny
mafft: DNA Sequence Alignment with MAFFT
mrbayes: Bayesian MCMC Tree Search with MrBayes
multistate: MULTISTATE
noi: Identification of MRCAs for Clades
pis: Number of Potentially-Informative Sites
prank: PRANK
raxml: Maximum Likelihood Tree Estimation with RAxML
raxml.partitions: Partition scheme for RAxML
rbeauti: XML Input Files for BEAST
read.beast: Read Bayesian Trees
read.beast.table: Extract node data from BEAST chronogram
read.fas: Read DNA Sequences
sister: Identification of Sister Nodes and Clades
tipHeights: Tip Heights in a Phylogenetic Tree
traitRate: Trait-Dependent Shifts in Molecular Rate
trimEnds: Trim Alignment Ends
write.fas: Write DNA Sequences to File
write.partitioned.nex: Write partitioned and commented NEXUS files

Functions

aliscore Man page Source code
code.simple.gaps Man page Source code
collapseUnsupportedEdges Man page Source code
delete.gaps Man page
deleteEmptyCells Man page Source code
deleteGaps Man page Source code
descendants Man page Source code
extractBEASTstats Man page Source code
extractMRBAYESstats Man page Source code
fillEndsWithN Man page
fixNodes Man page Source code
gblocks Man page Source code
ips Man page
ips-package Man page
ips.16S Man page
ips.28S Man page
ips.cox1 Man page
ips.tree Man page
mafft Man page Source code
mrbayes Man page Source code
mrbayes.mixed Man page Source code
multistate Man page
multistateMCMC Man page Source code
multistateML Man page Source code
noi Man page Source code
phylo2mafft Man page Source code
pis Man page Source code
prank Man page Source code
raxml Man page Source code
raxml.partitions Man page Source code
rbeauti Man page Source code
rbeauti.taxonset Man page Source code
read.beast Man page Source code
read.beast.table Man page Source code
read.fas Man page Source code
read.mrbayes Man page Source code
read.nex Man page Source code
read.phy Man page Source code
read.starbeast Man page Source code
read.xml Man page Source code
sister Man page Source code
terminal.clades Man page Source code
tipHeights Man page Source code
traitRate Man page Source code
traitRateOutput Man page Source code
traitRateParams Man page Source code
trimEnds Man page Source code
unresolve.clade Man page Source code
write.fas Man page Source code
write.nex Man page Source code
write.partitioned.nex Man page Source code
write.phy Man page Source code

Files

TODO
inst
inst/CITATION
NAMESPACE
data
data/ips.28S.rda
data/ips.16S.rda
data/ips.cox1.rda
data/ips.tree.rda
R
R/write.nex.R
R/write.phy.R
R/terminal.clades.R
R/read.fas.R
R/prank.R
R/noi.R
R/unresolve.clade.R
R/read.starbeast.R
R/multistateMCMC.R
R/aliscore.R
R/phylo2mafft.R
R/mrbayes.mixed.R
R/read.nex.R
R/pis.R
R/traitRateParams.R
R/deleteEmptyCells.R
R/traitRateOutput.R
R/rbeauti.taxonset.R
R/raxml.R
R/read.beast.table.R
R/code.simple.gaps.R
R/collapseUnsupportedEdges.R
R/read.xml.R
R/read.phy.R
R/deleteGaps.R
R/multistateML.R
R/fixNodes.R
R/raxml.partitions.R
R/extractMRBAYESstats.R
R/mafft.R
R/read.mrbayes.R
R/mrbayes.R
R/traitRate.R
R/trimEnds.R
R/read.beast.R
R/descendants.R
R/sister.R
R/rbeauti.R
R/write.partitioned.nex.R
R/tipHeights.R
R/write.fas.R
R/gblocks.R
R/extractBEASTstats.R
MD5
DESCRIPTION
ChangeLog
man
man/ips-internal.Rd
man/gblocks.Rd
man/deleteGaps.Rd
man/read.fas.Rd
man/ips.tree.Rd
man/ips-package.Rd
man/noi.Rd
man/traitRate.Rd
man/aliscore.Rd
man/tipHeights.Rd
man/sister.Rd
man/collapseUnsupportedEdges.Rd
man/prank.Rd
man/deleteEmptyCells.Rd
man/fixNodes.Rd
man/trimEnds.Rd
man/read.beast.table.Rd
man/mrbayes.Rd
man/ips.cox1.Rd
man/write.fas.Rd
man/read.beast.Rd
man/rbeauti.Rd
man/code.simple.gaps.Rd
man/multistate.Rd
man/raxml.Rd
man/mafft.Rd
man/descendants.Rd
man/ips.28S.Rd
man/raxml.partitions.Rd
man/pis.Rd
man/write.partitioned.nex.Rd
man/ips.16S.Rd
ips documentation built on May 19, 2017, 1:10 p.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.