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

Global functions
Call.rphast 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
makeObj.feat Source code
makeObj.hmm Source code
makeObj.msa Source code
makeObj.tm 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
rootLeaf.from.pointer.tm 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
rphast documentation built on Feb. 11, 2018, 5 p.m.