rphast-package	rphast-package
add.introns.feat	add.introns.feat
add.ls.mod	add.ls.mod
add.signals.feat	add.signals.feat
add.UTRs.feat	add.UTRs.feat
alphabet.msa	alphabet.msa
apply.bgc.sel	apply.bgc.sel
as.data.frame.feat	as.data.frame.feat
as.list.tm	as.list.tm
as.pointer.feat	as.pointer.feat
as.pointer.msa	as.pointer.msa
as.track.feat	as.track.feat
as.track.msa	as.track.msa
as.track.wig	as.track.wig
base.freq.msa	base.freq.msa
bgc.informative	bgc.informative
bgc.nucleotide.tests	bgc.nucleotide.tests
bgc.sel.factor	bgc.sel.factor
branchlength.tree	branchlength.tree
classify.muts.bgc	classify.muts.bgc
codon.clean.msa	codon.clean.msa
col.expected.subs.msa	col.expected.subs.msa
complement	complement
composition.feat	composition.feat
concat.msa	concat.msa
convert.coords.feat	convert.coords.feat
coord.range.msa	coord.range.msa
copy.feat	copy.feat
copy.msa	copy.msa
coverage.feat	coverage.feat
density.feat	density.feat
depth.tree	depth.tree
dim.feat	dim.feat
dim.msa	dim.msa
enrichment.feat	enrichment.feat
expected.subs.msa	expected.subs.msa
extract.feature.msa	extract.feature.msa
feat	feat
fix.semicolon.tree	fix.semicolon.tree
fix.start.stop.feat	fix.start.stop.feat
flatten.feat	flatten.feat
freq3x4.msa	freq3x4.msa
from.pointer.feat	from.pointer.feat
from.pointer.msa	from.pointer.msa
gc.content.msa	gc.content.msa
get.rate.matrix.params.tm	get.rate.matrix.params.tm
get4d.msa	get4d.msa
guess.format.msa	guess.format.msa
hist.feat	hist.feat
hmm	hmm
informative.regions.msa	informative.regions.msa
inverse.feat	inverse.feat
is.format.msa	is.format.msa
is.msa	is.msa
is.ordered.msa	is.ordered.msa
is.subst.mod.tm	is.subst.mod.tm
is.tm	is.tm
is.track	is.track
label.branches	label.branches
label.subtree	label.subtree
leafnames.tree	leafnames.tree
likelihood.msa	likelihood.msa
mod.backgd.tm	mod.backgd.tm
msa	msa
name.ancestors	name.ancestors
names.msa	names.msa
ncol.feat	ncol.feat
ncol.msa	ncol.msa
ninf.msa	ninf.msa
nothanks.rphast	nothanks.rphast
nrow.feat	nrow.feat
nrow.msa	nrow.msa
nstate.hmm	nstate.hmm
numleaf.tree	numleaf.tree
numnodes.tree	numnodes.tree
offset.msa	offset.msa
optim.rphast	optim.rphast
overlap.feat	overlap.feat
pairwise.diff.msa	pairwise.diff.msa
phastBias	phastBias
phastCons	phastCons
phyloFit	phyloFit
phyloP	phyloP
phyloP.prior	phyloP.prior
phyloP.sph	phyloP.sph
plot.feat	plot.feat
plot.gene	plot.gene
plot.lsmodel.tm	plot.lsmodel.tm
plot.msa	plot.msa
plot.rate.matrix	plot.rate.matrix
plot.tm	plot.tm
plot.track	plot.track
postprob.msa	postprob.msa
print.feat	print.feat
print.msa	print.msa
print.phastBiasResult	print.phastBiasResult
print.tm	print.tm
prune.tree	prune.tree
range.feat	range.feat
range.track	range.track
rbind.feat	rbind.feat
read.feat	read.feat
read.hmm	read.hmm
read.msa	read.msa
read.newick.tree	read.newick.tree
read.tm	read.tm
read.wig	read.wig
reflect.phylo.hmm	reflect.phylo.hmm
register.rphast	register.rphast
rename.tree	rename.tree
rescale.tree	rescale.tree
reverse.complement.msa	reverse.complement.msa
rphast	rphast-package
sample.msa	sample.msa
score.hmm	score.hmm
set.rate.matrix.tm	set.rate.matrix.tm
setup.branch.site.tm	setup.branch.site.tm
simulate.msa	simulate.msa
smooth.wig	smooth.wig
sort.feat	sort.feat
split.by.feature.msa	split.by.feature.msa
split.feat	split.feat
state.freq.msa	state.freq.msa
strip.gaps.msa	strip.gaps.msa
sub.msa	sub.msa
subst.mods	subst.mods
subtree	subtree
summary.feat	summary.feat
summary.msa	summary.msa
summary.tm	summary.tm
summary.tree	summary.tree
tagval	tagval
tagval.feat	tagval.feat
tm	tm
total.expected.subs.msa	total.expected.subs.msa
translate.msa	translate.msa
unapply.bgc.sel	unapply.bgc.sel
unique.feat	unique.feat
write.feat	write.feat
write.hmm	write.hmm
write.msa	write.msa
write.tm	write.tm
write.wig	write.wig
write.wig.feat	write.wig.feat
[.msa	square-bracket-msa
[<-.msa	square-bracket-assign-msa
