phyclust-package	00_phyclust-package
.boundary.method	11_d.boundary.method
.code.type	11_d.code.type
.Color	11_d.Color
.edist.model	11_d.edist.model
.em.method	11_d.em.method
.EMC	11_d.EMC
.EMControl	11_d.EMControl
.identifier	11_d.identifier
.init.method	11_d.init.method
.init.procedure	11_d.init.procedure
.nucleotide	11_d.standard.code
.show.option	11_d.show.option
.snp	11_d.standard.code
.substitution	11_d.substitution
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
chkdim.Add.fun	zz_all.internal.tzeng
chkdim.Multiply.fun	zz_all.internal.tzeng
Class ms	ms
Class phyclust	phyclust
Class phylo	as.star.tree
Class seq.data	seq.data.toy
Class seqgen	seqgen
code2nid	code2nid
code2snp	code2snp
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.toy
final.BigMatB.fun	zz_all.internal.tzeng
final.BigMatB.matC.fun	zz_all.internal.tzeng
find.best	find.best
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.matD.matEI.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
haplo.score.RD.unphased.fun	zz_all.internal.tzeng
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
nid2code	code2nid
nid2sid	code2snp
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
plotdots	plotdots
plotfd	zz_all.internal
plothist	plothist
plothist.my	zz_all.internal
plotnj	plotnj
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
read.fasta	file.read
read.fasta.nucleotide	file.read
read.phylip	file.read
read.phylip.nucleotide	file.read
read.phylip.snp	file.read
read.seqgen	read.seqgen
rescale.rooted.tree	rescale.rooted.tree
RRand	RRand
seq.data.toy	seq.data.toy
seqgen	seqgen
sid2nid	code2snp
sid2snp	snp2sid
snp2code	code2snp
snp2sid	snp2sid
summary.phyclust	print.summary
translate.EMC	zz_all.internal
translate.ret	zz_all.internal
unstrsplit	zz_all.internal
write.fasta	file.write
write.fasta.nucleotide	file.write
write.phylip	file.write
write.phylip.nucleotide	file.write
write.phylip.snp	file.write
zero.mat.fun	zz_all.internal.tzeng
