ips-package	ips-package
aliscore	aliscore
are.tips.consecutive	ips-internal
assembleDataNode	ips-internal
assembleDistributionNode	ips-internal
assembleInitNode	ips-internal
assembleLoggers	ips-internal
assembleOperators	ips-internal
assembleStateNode	ips-internal
code.simple.gaps	code.simple.gaps
collapseUnsupportedEdges	collapseUnsupportedEdges
del.miss	del.miss
deleteEmptyCells	deleteEmptyCells
deleteGaps	deleteGaps
descendants	descendants
DNAbin2index	DNAbin2index
eoi	oi
extractBEASTstats	ips-internal
extractMRBAYESstats	ips-internal
fixNodes	fixNodes
forceEqualTipHeights	forceEqualTipHeights
formatSet	ips-internal
gblocks	gblocks
index2DNAbin	index2DNAbin
ips	ips-package
ips.16S	ips.16S
ips.28S	ips.28S
ips.cox1	ips.cox1
ips.tree	ips.tree
mafft	mafft
mafft.merge	mafft.merge
matrixBlock	ips-internal
mrbayes	mrbayes
mrbayes.lset	mrbayes.lset
mrbayes.mcmc	mrbayes.mcmc
mrbayes.prset	mrbayes.prset
multistate	multistate
multistateMCMC	multistate
multistateML	multistate
neighboringPairs	neighboringPairs
noi	oi
ntip	ntip
oi	oi
partitionfinder	partitionfinder
pathd8	pathd8
phylo2mafft	phylo2mafft
phylo2mst	phylo2mst
pis	pis
prank	prank
raxml	raxml
raxml.partitions	raxml.partitions
rbeauti	rbeauti
rbeauti.taxonset	ips-internal
rc	ips-internal
rc.core	ips-internal
read	read
read.beast	read.beast
read.beast.table	read.beast.table
read.fas	read
read.mrbayes	read.beast
read.nex	read
read.phy	read
read.starbeast	read.beast
read.xml	ips-internal
setClock	ips-internal
setMCMC	ips-internal
sister	sister
splitIntoClades	splitIntoClades
str2cha	ips-internal
terminal.clades	ips-internal
terminalSisters	terminalSisters
tipHeights	tipHeights
traitRate	traitRate
traitRateOutput	ips-internal
traitRateParams	ips-internal
trimEnds	trimEnds
unlistFirstLevel	unlistFirstLevel
unresolve.clade	ips-internal
write.fas	write.fas
write.nex	write.fas
write.phy	write.fas
