phyclust-package	00_phyclust-package
.amino.acid	11_d.standard.code
.boundary.method	11_d.boundary.method
.code.type	11_d.code.type
.codon	11_d.standard.code
.Color	11_d.Color
.edist.model	11_d.edist.model
.em.method	11_d.em.method
.EMC	11_d.EMC
.EMControl	11_d.EMControl
.genetic.code	11_d.standard.code
.identifier	11_d.identifier
.init.method	11_d.init.method
.init.procedure	11_d.init.procedure
.label.method	11_d.label.method
.missing.code	11_d.standard.code
.nucleotide	11_d.standard.code
.se.model	11_d.se.model
.show.option	11_d.show.option
.snp	11_d.standard.code
.substitution.model	11_d.substitution
.tzengEnv	zz_all.internal.tzeng
acode2aid	nid.aid.cid
acode2aid.default	zz_all.internal
acode2aid.list	zz_all.internal
aid2acode	nid.aid.cid
aid2acode.default	zz_all.internal
aid2acode.list	zz_all.internal
as.star.tree	as.star.tree
bootstrap.merge.seq	zz_all.internal
bootstrap.seq	bootstrap.seq
bootstrap.seq.data	bootstrap.seq.data
bootstrap.seq.nucleotide	zz_all.internal
bootstrap.seq.snp	zz_all.internal
bootstrap.star.tree	zz_all.internal
bootstrap.star.trees	bootstrap.star.trees
bootstrap.star.trees.seq	bootstrap.star.trees.seq
check.EMC	zz_all.internal
check.label	zz_all.internal
chkdim.Add.fun	zz_all.internal.tzeng
chkdim.Multiply.fun	zz_all.internal.tzeng
cid2aid	nid.aid.cid
cid2aid.default	zz_all.internal
cid2aid.list	zz_all.internal
Class baseml	paml.baseml
Class ms	ms
Class phyclust	phyclust
Class phylo	as.star.tree
Class seq.data	seq.data
Class seqgen	seqgen
code2nid	code2nid
code2nid.default	zz_all.internal
code2nid.list	zz_all.internal
code2snp	code2snp
code2snp.default	zz_all.internal
code2snp.list	zz_all.internal
construct.bigB.dPI	zz_all.internal.tzeng
construct.dB.list.fun	zz_all.internal.tzeng
convert.QA.to.vect	zz_all.internal
Data Crohn's Disease	data.phylip.crohn
Data Pony 524	data.phylip.pony
Data Pony 625	data.fasta.pony
Data Toy	seq.data
final.BigMatB.fun	zz_all.internal.tzeng
final.BigMatB.matC.fun	zz_all.internal.tzeng
find.best	find.best
find.consensus	find.consensus
Format fasta	data.fasta.pony
Format phylip	data.phylip.pony
gen.equal.star.anc.dec	gen.equal.star.anc.dec
gen.seq.HKY	gen.seq
gen.seq.SNP	gen.seq
gen.star.tree	gen.star.tree
gen.unit.K	gen.unit.K
get.allpossROUTE.fun	zz_all.internal.tzeng
get.BB.fun	zz_all.internal.tzeng
get.deriBigMatB.fun	zz_all.internal.tzeng
get.fullBB.fun	zz_all.internal.tzeng
get.I.fun	zz_all.internal.tzeng
get.ini.possHap.hapReserv.fun	zz_all.internal.tzeng
get.medBB.skip.fun	zz_all.internal.tzeng
get.preBB.skip.fun	zz_all.internal.tzeng
get.rooted.tree.height	get.rooted.tree.height
get.step.mut.fun	zz_all.internal.tzeng
get.subPI.fun	zz_all.internal.tzeng
getBigMatB.fun	zz_all.internal.tzeng
getcut.fun	getcut.fun
getI13.fun	zz_all.internal.tzeng
getPIstar.fun	zz_all.internal.tzeng
haplo.phase.known	zz_all.internal.tzeng
haplo.post.prob	haplo.post.prob
I33Inv.fun	zz_all.internal.tzeng
index.k.fun	zz_all.internal.tzeng
ms	ms
my.cat	zz_all.internal
my.format	zz_all.internal
my.print	zz_all.internal
nid2aid	nid.aid.cid
nid2aid.default	zz_all.internal
nid2aid.list	zz_all.internal
nid2cid	nid.aid.cid
nid2cid.default	zz_all.internal
nid2cid.list	zz_all.internal
nid2code	code2nid
nid2code.default	zz_all.internal
nid2code.list	zz_all.internal
nid2sid	code2snp
paml.baseml	paml.baseml
paml.baseml.control	paml.baseml
paml.baseml.show.default	paml.baseml
phyclust	phyclust
phyclust.e.step	phyclust.e.step
phyclust.edist	phyclust.edist
phyclust.em.step	phyclust.em.step
phyclust.logL	phyclust.logL
phyclust.m.step	phyclust.m.step
phyclust.Pt	phyclust.Pt
phyclust.se	phyclust.se
phyclust.se.update	phyclust.se.update
phyclust.update	phyclust.update
plotdots	plotdots
plotfd	zz_all.internal
plotgaps	plotgaps
plothist	plothist
plothist.my	zz_all.internal
plotnj	plotnj
plotstruct	plotstruct
print.baseml	print.summary
print.ms	print.summary
print.phyclust	print.summary
print.Pt	print.summary
print.RRand	print.summary
print.seq.data	print.summary
print.seqgen	print.summary
prune.Mu	prune.Mu
read.fasta	file.read
read.fasta.format	file.read
read.phylip	file.read
read.phylip.format	file.read
read.seqgen	read.seqgen
rescale.rooted.tree	rescale.rooted.tree
RRand	RRand
seq.data.gap	seq.data
seq.data.toy	seq.data
seqgen	seqgen
sid2nid	code2snp
sid2snp	snp2sid
sid2snp.default	zz_all.internal
sid2snp.list	zz_all.internal
snp2code	code2snp
snp2code.default	zz_all.internal
snp2code.list	zz_all.internal
snp2sid	snp2sid
snp2sid.default	zz_all.internal
snp2sid.list	zz_all.internal
summary.phyclust	print.summary
translate.EMC	zz_all.internal
translate.EMC.se	zz_all.internal
translate.ret	zz_all.internal
translate.ret.se	zz_all.internal
unstrsplit	zz_all.internal
write.fasta	file.write
write.fasta.format	file.write
write.paml	file.write
write.paml.format	file.write
write.phylip	file.write
write.phylip.format	file.write
zero.mat.fun	zz_all.internal.tzeng
