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.

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

View on CRAN

Functions

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

Files

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

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

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

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