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
assembleTreeNode	ips-internal
beastLog	beastLog
blastn	blastn
code.simple.gaps	code.simple.gaps
collapseUnsupportedEdges	collapseUnsupportedEdges
combMyTree	combMyTree
del.miss	del.miss
deleteEmptyCells	EmptyCells
deleteGaps	deleteGaps
descendants	descendants
DNAbin2index	DNAbin2index
EmptyCells	EmptyCells
eoi	oi
extractBEASTstats	ips-internal
extractMRBAYESstats	ips-internal
fixNodes	fixNodes
forceEqualTipHeights	forceEqualTipHeights
formatSet	ips-internal
gblocks	gblocks
identifyEmptyCells	EmptyCells
index2DNAbin	index2DNAbin
ips	ips-package
ips.16S	ips.16S
ips.28S	ips.28S
ips.cox1	ips.cox1
ips.tree	ips.tree
log_list	ips-internal
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
operator	ips-internal
operator_list	ips-internal
parameter	ips-internal
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	rc
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
