Man pages for heibl/ips
Interfaces to Phylogenetic Software in R

aliscoreMasking of Sequence Alignments with ALISCORE
code.simple.gapsSimple Gap/Indel Coding
collapseUnsupportedEdgesCollapse Unsupported Edges/Branches in a Phylogeny
deleteEmptyCellsDelete Spurious Rows and Columns from DNA Alignments
deleteGapsRemove Gap Positions From DNA Sequences
del.missDelete Missing Data from DNA Sequences
descendantsDescendants of an Internal Node in a Phylogeny
DNAbin2indexConversion of DNAbin to Index
fixNodesStandard Node Numbering in Phylo Objects
forceEqualTipHeightsEqual Tip Heights
gblocksMasking of Sequence Alignments with GBLOCKS
index2DNAbinConversion of Index to DNAbin
ips.16SBark Beetle 16S Sequences
ips.28SBark Beetle 28S Sequences
ips.cox1Bark Beetle COX1 Sequences
ips-internalInternal IPS Functions
ips-packageInterfaces to Phylogenetic Software
ips.treeIps Phylogeny
mafftSequence Alignment with MAFFT
mafft.mergeProfile Alignment with MAFFT
mrbayesBayesian MCMC Tree Search with MrBayes
mrbayes.lsetModel Settings for MrBayes
mrbayes.mcmcMCMC Settings for MrBayes
mrbayes.prsetSet Priors for MrBayes
multistateMULTISTATE
neighboringPairsNeighboring Nodes in a Minimumn Spanning Tree
ntipNumbers of Tips of (Sub)trees
oiIdentification of Stem-Lineage-Edges and MRCAs
partitionfinderPartitionFinder
pathd8PATHd8
phylo2mafftConvert Trees for MAFFT
phylo2mstConversion from PHYLO to MST Object
pisNumber of Potentially-Informative Sites
prankPRANK
raxmlMaximum Likelihood Tree Estimation with RAxML
raxml.partitionsPartition scheme for RAxML
rbeautiXML Input Files for BEAST
readReading Sequence Files
read.beastRead Bayesian Trees
read.beast.tableExtract node data from BEAST chronogram
sisterIdentification of Sister Nodes and Clades
splitIntoCladesFind Monophyletic Subsets in Species Lists
terminalSistersFind Pairs of Sister Species
tipHeightsTip Heights in a Phylogenetic Tree
traitRateTrait-Dependent Shifts in Molecular Rate
trimEndsTrim Alignment Ends
unlistFirstLevelUnlist To First Level Only
write.fasWrite DNA Sequences to File
heibl/ips documentation built on Sept. 23, 2018, 3:22 p.m.