API for ips
Interfaces to Phylogenetic Software in R

Global functions
DNAbin2index	Man page Source code
EmptyCells	Man page
LogNormalPrior	Source code
aliscore	Man page Source code
are.tips.consecutive	Man page Source code
assembleDataNode	Man page Source code
assembleDistributionNode	Man page Source code
assembleInitNode	Man page Source code
assembleLikelihoodNode	Source code
assembleLoggers	Man page Source code
assembleOperators	Man page Source code
assemblePriorNode	Source code
assembleStateNode	Man page Source code
assembleTaxonSetPrior	Source code
assembleTreeNode	Man page Source code
beastLog	Man page Source code
blastn	Man page Source code
code.simple.gaps	Man page Source code
collapseUnsupportedEdges	Man page Source code
combMyTree	Man page Source code
del.miss	Man page
deleteEmptyCells	Man page Source code
deleteGaps	Man page Source code
descendants	Man page Source code
eoi	Man page Source code
extractBEASTstats	Man page Source code
extractMRBAYESstats	Man page Source code
findORF	Source code
fixNodes	Man page Source code
forceEqualTipHeights	Man page Source code
formatSet	Man page Source code
gammaPrior	Source code
gblocks	Man page Source code
identifyEmptyCells	Man page Source code
index2DNAbin	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
log_list	Man page
mafft	Man page Source code
mafft.merge	Man page Source code
matrixBlock	Man page Source code
mrbayes	Man page Source code
mrbayes.lset	Man page Source code
mrbayes.mcmc	Man page Source code
mrbayes.prset	Man page Source code
multistate	Man page
multistateMCMC	Man page Source code
multistateML	Man page Source code
neighboringPairs	Man page Source code
noi	Man page Source code
ntip	Man page Source code
oi	Man page
operator	Man page Source code
operator_list	Man page
parameter	Man page Source code
partitionfinder	Man page Source code
pathd8	Man page Source code
phylo2mafft	Man page Source code
phylo2mst	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
rc	Man page Source code
rc.core	Man page
read	Man page
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
realParameter	Source code
setClock	Man page Source code
setMCMC	Man page Source code
sister	Man page Source code
splitIntoClades	Man page Source code
str2cha	Man page Source code
terminal.clades	Man page Source code
terminalSisters	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
uniformPrior	Source code
unlistFirstLevel	Man page Source code
unresolve.clade	Man page Source code
write.fas	Man page Source code
write.nex	Man page Source code
write.phy	Man page Source code