API for rphast
Interface to 'PHAST' Software for Comparative Genomics

Global functions
.Call.rphast	Source code
.makeObj.feat	Source code
.makeObj.hmm	Source code
.makeObj.msa	Source code
.makeObj.tm	Source code
.rootLeaf.from.pointer.tm	Source code
[.msa	Man page
[<-.msa	Man page
add.UTRs.feat	Man page Source code
add.introns.feat	Man page Source code
add.ls.mod	Man page Source code
add.signals.feat	Man page Source code
alphabet.msa	Man page Source code
apply.bgc.sel	Man page Source code
as.data.frame.feat	Man page Source code
as.list.tm	Man page Source code
as.pointer.feat	Man page Source code
as.pointer.hmm	Source code
as.pointer.msa	Man page Source code
as.pointer.tm	Source code
as.tm.list	Source code
as.track.feat	Man page Source code
as.track.msa	Man page Source code
as.track.wig	Man page Source code
base.freq.msa	Man page Source code
bgc.informative	Man page Source code
bgc.nucleotide.tests	Man page Source code
bgc.sel.factor	Man page Source code
branchlength.tree	Man page Source code
check.arg	Source code
classify.muts.bgc	Man page Source code
codon.clean.msa	Man page Source code
col.expected.subs.msa	Man page Source code
complement	Man page Source code
composition.feat	Man page Source code
concat.msa	Man page Source code
convert.coords.feat	Man page Source code
coord.range.msa	Man page Source code
copy.feat	Man page Source code
copy.msa	Man page Source code
coverage.feat	Man page Source code
density.feat	Man page Source code
depth.tree	Man page Source code
dim.feat	Man page Source code
dim.msa	Man page Source code
enrichment.feat	Man page Source code
expected.subs.msa	Man page Source code
extract.feature.msa	Man page Source code
feat	Man page Source code
fill.in.array.lol	Source code
fix.freq.hmm	Source code
fix.semicolon.tree	Man page Source code
fix.start.stop.feat	Man page Source code
flatten.feat	Man page Source code
freeall.rphast	Source code
freq3x4.msa	Man page Source code
from.pointer.feat	Man page Source code
from.pointer.hmm	Source code
from.pointer.lsmodel.tm	Source code
from.pointer.msa	Man page Source code
from.pointer.one.lsmodel.tm	Source code
from.pointer.tm	Source code
gc.content.msa	Man page Source code
get.rate.matrix.params.tm	Man page Source code
get4d.msa	Man page Source code
guess.format.msa	Man page Source code
hist.feat	Man page Source code
hmm	Man page Source code
informative.regions.msa	Man page Source code
inverse.feat	Man page Source code
is.format.msa	Man page Source code
is.msa	Man page Source code
is.ordered.msa	Man page Source code
is.subst.mod.tm	Man page Source code
is.tm	Man page Source code
is.track	Man page Source code
label.branches	Man page Source code
label.subtree	Man page Source code
leafnames.tree	Man page Source code
likelihood.msa	Man page Source code
mod.backgd.tm	Man page Source code
msa	Man page Source code
name.ancestors	Man page Source code
names.msa	Man page Source code
ncol.feat	Man page Source code
ncol.msa	Man page Source code
ninf.msa	Man page Source code
nothanks.rphast	Man page Source code
nrow.feat	Man page Source code
nrow.msa	Man page Source code
nstate.hmm	Man page Source code
numleaf.tree	Man page Source code
numnodes.tree	Man page Source code
offset.msa	Man page Source code
optim.rphast	Man page Source code
overlap.feat	Man page Source code
pairwise.diff.msa	Man page Source code
phastBias	Man page Source code
phastCons	Man page Source code
phastCons.call	Source code
phyloFit	Man page Source code
phyloP	Man page Source code
phyloP.call	Source code
phyloP.prior	Man page Source code
phyloP.sph	Man page Source code
plot.feat	Man page Source code
plot.gene	Man page Source code
plot.lsmodel.tm	Man page Source code
plot.msa	Man page Source code
plot.rate.matrix	Man page Source code
plot.tm	Man page Source code
plot.track	Man page Source code
postprob.msa	Man page Source code
print.feat	Man page Source code
print.msa	Man page Source code
print.phastBiasResult	Man page Source code
print.tm	Man page Source code
prune.tree	Man page Source code
range.feat	Man page Source code
range.track	Man page Source code
rbind.feat	Man page Source code
read.feat	Man page Source code
read.hmm	Man page Source code
read.msa	Man page Source code
read.newick.tree	Man page Source code
read.tm	Man page Source code
read.wig	Man page Source code
reflect.phylo.hmm	Man page Source code
register.rphast	Man page Source code
rename.tree	Man page Source code
rescale.tree	Man page Source code
reverse.complement.msa	Man page Source code
rphast	Man page
rphast-package	Man page
rphast.simplify.list	Source code
sample.msa	Man page Source code
score.hmm	Man page Source code
set.rate.matrix.tm	Man page Source code
setup.branch.site.tm	Man page Source code
simulate.msa	Man page Source code
smooth.wig	Man page Source code
sort.feat	Man page Source code
split.by.feature.msa	Man page Source code
split.feat	Man page Source code
state.freq.msa	Man page Source code
stop.if.not.valid.hmm	Source code
strip.gaps.msa	Man page Source code
sub.msa	Man page Source code
subst.mods	Man page Source code
subtree	Man page Source code
summary.feat	Man page Source code
summary.msa	Man page Source code
summary.tm	Man page Source code
summary.tree	Man page Source code
tagval	Man page Source code
tagval.feat	Man page Source code
tm	Man page Source code
total.expected.subs.msa	Man page Source code
translate.msa	Man page Source code
unapply.bgc.sel	Man page Source code
unique.feat	Man page Source code
write.feat	Man page Source code
write.hmm	Man page Source code
write.msa	Man page Source code
write.tm	Man page Source code
write.wig	Man page Source code
write.wig.feat	Man page Source code