allSitePattern	phyDat
allTrees	allTrees
Ancestors	Ancestors
as.character.phyDat	phyDat
as.DNAbin.phyDat	phyDat
as.phyDat	phyDat
as.phyDat.DNAbin	phyDat
bootstrap.phyDat	bootstrap.pml
bootstrap.pml	bootstrap.pml
Children	Ancestors
chloroplast	chloroplast
Descendants	Ancestors
designSplits	designTree
designTree	designTree
dfactorial	dfactorial
dist.hamming	dist.hamming
dist.logDet	dist.hamming
dist.ml	dist.hamming
distanceHadamard	distanceHadamard
fhm	hadamard
fitch	parsimony
h2st	hadamard
h4st	hadamard
hadamard	hadamard
Laurasiatherian	Laurasiatherian
ldfactorial	dfactorial
NJ	NJ
nni	nni
optim.parsimony	parsimony
optim.pml	pml
pace	parsimony
parsimony	parsimony
phyDat	phyDat
plotBS	bootstrap.pml
pml	pml
pmlCluster	pmlCluster
pmlMix	pmlMix
pmlPart	pmlPart
pmlPen	pmlMix
PNJ	parsimony
read.aa	read.aa
read.phyDat	phyDat
RF.dist	treedist
rNNI	nni
rSPR	nni
sankoff	parsimony
SH.test	SH.test
Siblings	Ancestors
simSeq	simSeq
splitsNetwork	splitsNetwork
treedist	treedist
UNJ	NJ
upgma	upgma
write.nexus.splits	hadamard
write.phyDat	phyDat
yeast	yeast
[.phyDat	phyDat
