ips: Interfaces to Phylogenetic Software in R

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

Author
Christoph Heibl <christoph.heibl@gmx.net>
Date of publication
2014-11-10 00:38:44
Maintainer
Christoph Heibl <christoph.heibl@gmx.net>
License
GPL (>= 2)
Version
0.0-7

View on CRAN

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

Files in this package

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