rphast: Interface to PHAST Software for Comparative Genomics

Provides an R interface to the PHAST software (Phylogenetic Analysis with Space/Time Models). It can be used for many types of analysis in comparative and evolutionary genomics, such as estimating models of evolution from sequence data, scoring alignments for conservation or acceleration, and predicting elements based on conservation or custom phylogenetic hidden Markov models. It can also perform many basic operations on multiple sequence alignments and phylogenetic trees.

AuthorMelissa Hubisz, Katherine Pollard, and Adam Siepel
Date of publication2016-08-16 00:25:52
MaintainerMelissa Hubisz <mjhubisz@cornell.edu>
LicenseBSD_3_clause + file LICENSE
Version1.6.5
http://compgen.cshl.edu/rphast

View on CRAN

Man pages

add.introns.feat: Add introns to features

add.ls.mod: Add a lineage-specific model

add.signals.feat: Add start/stop codon, 3'/5' splice signals to features

add.UTRs.feat: Add UTRs to features

alphabet.msa: MSA Alphabet

apply.bgc.sel: Apply bgc+selection parameters to a matrix

as.data.frame.feat: Features to Data Frame

as.list.tm: Tree Model to List

as.pointer.feat: Features To Pointer

as.pointer.msa: MSA To Pointer

as.track.feat: Create a features track

as.track.msa: Create an alignment track

as.track.wig: Create a wig track

base.freq.msa: Get the frequencies of characters in an alignment

bgc.informative: Return features indicating regions informative for bgc

bgc.nucleotide.tests: Do maximum likelihood analysis for gBGC and selection using...

bgc.sel.factor: BGC+selection factor

branchlength.tree: Get the total length of the edges of a tree

classify.muts.bgc: Count the number of mutations of each gBGC type on each...

codon.clean.msa: Clean an alignment for codon analysis

col.expected.subs.msa: Obtain expected number of substitutions on each branch for...

complement: complement

composition.feat: Composition of features with respect to annotations

concat.msa: Concatenate msa objects

convert.coords.feat: Convert coordinates from one frame of reference to another

coord.range.msa: Obtain the range of coordinates in a MSA objects

copy.feat: Features copy

copy.msa: MSA copy

coverage.feat: Features coverage

density.feat: Features kernel density

depth.tree: Get the distance from a node to the root of a tree

dim.feat: Feature dimensions

dim.msa: Returns the dimensions of an msa object as (# of species, #...

enrichment.feat: Enrichment of features with respect to annotation types

expected.subs.msa: Obtain expected number of substitutions on each branch and...

extract.feature.msa: Extract features from an MSA object

feat: Features Objects

fix.semicolon.tree: Add a semi-colon to end of tree string

fix.start.stop.feat: Fix start and stop signals

flatten.feat: Combine adjacent features with the same "feature" field

freq3x4.msa: Get codon frequencies based on 3x4 model

from.pointer.feat: Convert a features object from C memory (external pointer) to...

from.pointer.msa: MSA From Pointer

gc.content.msa: Get the fraction of G's and C's in an alignment

get4d.msa: Extract fourfold degenerate sites from an MSA object

get.rate.matrix.params.tm: Get the parameters describing a rate matrix

guess.format.msa: MSA Guess Format

hist.feat: plot histogram of feature lengths

hmm: Create an rphast HMM object

informative.regions.msa: Get informative regions of an alignment

inverse.feat: Get inverse features

is.format.msa: Check an MSA Format String

is.msa: Check an MSA object

is.ordered.msa: MSA is Ordered?

is.subst.mod.tm: Check Substitution Model Strings

is.tm: Tree Models

is.track: Is this a track?

label.branches: Label tree branches

label.subtree: Label subtree

leafnames.tree: Get the names of a tree's leaf nodes

likelihood.msa: MSA Likelihood

mod.backgd.tm: Adjust tree model background frequencies while maintaining...

msa: MSA Objects

name.ancestors: Name Ancestral Nodes

names.msa: MSA Sequence Names

ncol.feat: Number of Columns in Features

ncol.msa: MSA Sequence Length.

ninf.msa: The number of informative columns in an alignment

nothanks.rphast: Stop rphast registration reminders

nrow.feat: Number of Features

nrow.msa: MSA Number of Sequences

nstate.hmm: HMM number of states

numleaf.tree: Number of leaves in a Tree

numnodes.tree: Number of Nodes in a Tree

offset.msa: MSA Index Offset

optim.rphast: Optimize using phast's optimization code

overlap.feat: Feature overlap

pairwise.diff.msa: Get pairwise differences per site between sequences

phastBias: phastBias

phastCons: Produce conservation scores and identify conserved elements,...

phyloFit: Fit a Phylogenetic model to an alignment...

phyloP: phyloP (basewise or by feature)

phyloP.prior: phyloP prior

phyloP.sph: phyloP SPH

plot.feat: Features plot

plot.gene: Gene plot

plot.lsmodel.tm: Make a bubble plot of a lineage-specific transition matrix of...

plot.msa: Plot an alignment

plot.rate.matrix: Make a bubble plot of a transition matrix

plot.tm: Make a bubble plot of the transition matrix for a tree model.

plot.track: Make browser-like plot in rphast

postprob.msa: Obtain posterior probilities of every state at every node

print.feat: Printing a features Object

print.msa: Printing MSA objects

print.phastBiasResult: Pretty-print the phastBias result list without spilling giant...

print.tm: Printing Tree Models

prune.tree: Prune a Tree

range.feat: Features range

range.track: Get the coordinate range of a list of RPHAST results

rbind.feat: concatenate feature objects

read.feat: Read a Feature File (GFF, BED, or GenePred)

read.hmm: Read an HMM object from a file

read.msa: Reading an MSA Object

read.newick.tree: Read a Newick Tree from a File

read.tm: Read a Tree Model

read.wig: Read a wig file

reflect.phylo.hmm: Reflect a phylo-hmm across a strand

register.rphast: Register RPHAST

rename.tree: Tree Node Renaming

rescale.tree: Scale a Tree or Subtree

reverse.complement.msa: Reverse complement a multiple sequence alignment

rphast-package: Interface to PHAST Software for Comparative Genomics

sample.msa: Sample columns from an MSA

score.hmm: Score an alignment using a general phylo-HMM

set.rate.matrix.tm: Set the rate matrix of a tree model using model-specific...

setup.branch.site.tm: Set up a tree model for branch site selection analysis

simulate.msa: Simulate a MSA given a tree model and HMM.

smooth.wig: Smooth a wig plot in rphast

sort.feat: Sort a GFF

split.by.feature.msa: Split an MSA by feature

split.feat: Split features by length

square-bracket-assign-msa: Replace subsets of an alignment

square-bracket-msa: Extract, replace, reorder MSA

state.freq.msa: Get the observed frequencies of states in an alignment

strip.gaps.msa: MSA Strip Gaps

sub.msa: MSA Subset

subst.mods: List PHAST Substitution Models

subtree: Subtree

summary.feat: Features Summary

summary.msa: MSA Summary

summary.tm: Tree Model Summary

summary.tree: Get a summary of a Newick-formatted tree, edge lengths, node...

tagval: Extract value from tag-value formatted attributes

tagval.feat: Extract value from tag-value formatted attribute in features...

tm: Tree Models

total.expected.subs.msa: Obtain expected number of substitutions of each type on each...

translate.msa: Get amino acid sequences from an alignment

unapply.bgc.sel: Unapply bgc+selection parameters from a matrix

unique.feat: Remove overlapping genes

write.feat: Writing a features Object

write.hmm: Write an HMM object to a file

write.msa: Writing MSA Objects to Files

write.tm: Wrting Tree Models

write.wig: Writing a wig file

write.wig.feat: Write a features object in fixedStep wig format

Functions

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

Files

rphast
rphast/inst
rphast/inst/examples
rphast/inst/examples/summary-tree.R
rphast/inst/examples/likelihood-msa.R
rphast/inst/examples/write-wig.R
rphast/inst/examples/sub-msa.R
rphast/inst/examples/phastCons.R
rphast/inst/examples/col-expected-subs-msa.R
rphast/inst/examples/score-hmm.R
rphast/inst/examples/as-data-frame-feat.R
rphast/inst/examples/split-by-feature-msa.R
rphast/inst/examples/as-pointer-feat.R
rphast/inst/examples/summary-tm.R
rphast/inst/examples/read-msa.R
rphast/inst/examples/subtree.R
rphast/inst/examples/reflect-phylo-hmm.R
rphast/inst/examples/convert-coords-feat.R
rphast/inst/examples/write-msa.R
rphast/inst/examples/is-subst-mod-tm.R
rphast/inst/examples/phyloP.R
rphast/inst/examples/subst-mods.R
rphast/inst/examples/plot-msa.R
rphast/inst/examples/hmm.R
rphast/inst/examples/numnodes-tree.R
rphast/inst/examples/as-pointer-msa.R
rphast/inst/examples/nrow-feat.R
rphast/inst/examples/prune-tree.R
rphast/inst/examples/offset-msa.R
rphast/inst/examples/fix-semicolon-tree.R
rphast/inst/examples/feat.R
rphast/inst/examples/names-msa.R
rphast/inst/examples/coverage-feat.R
rphast/inst/examples/plot-lsmodel-tm.R
rphast/inst/examples/postprob-msa.R
rphast/inst/examples/square-bracket-assign-msa.R
rphast/inst/examples/informative-regions-msa.R
rphast/inst/examples/fix-start-stop-feat.R
rphast/inst/examples/expected-subs-msa.R
rphast/inst/examples/mod-backgd-tm.R
rphast/inst/examples/write-hmm.R
rphast/inst/examples/write-wig-feat.R
rphast/inst/examples/strip-gaps-msa.R
rphast/inst/examples/add-introns-feat.R
rphast/inst/examples/get4d-msa.R
rphast/inst/examples/sample-msa.R
rphast/inst/examples/phyloP-prior.R
rphast/inst/examples/square-bracket-msa.R
rphast/inst/examples/tm.R
rphast/inst/examples/print-msa.R
rphast/inst/examples/simulate-msa.R
rphast/inst/examples/ncol-msa.R
rphast/inst/examples/label-branches.R
rphast/inst/examples/translate-msa.R
rphast/inst/examples/as-track-feat.R
rphast/inst/examples/read-feat.R
rphast/inst/examples/add-signals-feat.R
rphast/inst/examples/nrow-msa.R
rphast/inst/examples/summary-msa.R
rphast/inst/examples/is-ordered-msa.R
rphast/inst/examples/read-hmm.R
rphast/inst/examples/read-newick-tree.R
rphast/inst/examples/name-ancestors.R
rphast/inst/examples/alphabet-msa.R
rphast/inst/examples/rescale-tree.R
rphast/inst/examples/dim-feat.R
rphast/inst/examples/print-tm.R
rphast/inst/examples/phyloFit.R
rphast/inst/examples/add-UTRs-feat.R
rphast/inst/examples/write-feat.R
rphast/inst/examples/plot-tm.R
rphast/inst/examples/rename-tree.R
rphast/inst/examples/msa.R
rphast/inst/examples/as-list-tm.R
rphast/inst/examples/plot-feat.R
rphast/inst/examples/plot-gene.R
rphast/inst/examples/read-tm.R
rphast/inst/examples/total-expected-subs-msa.R
rphast/inst/examples/from-pointer-msa.R
rphast/inst/examples/overlap-feat.R
rphast/inst/examples/label-subtree.R
rphast/inst/examples/summary-feat.R
rphast/inst/examples/guess-format-msa.R
rphast/inst/examples/ncol-feat.R
rphast/inst/examples/write-tm.R
rphast/inst/examples/tagval.R
rphast/inst/examples/is-format-msa.R
rphast/inst/examples/tagval-feat.R
rphast/inst/extdata
rphast/inst/extdata/NRSF.zip
rphast/inst/extdata/examples.zip
rphast/inst/doc
rphast/inst/doc/vignette1.Rnw
rphast/inst/doc/vignette4.Rnw
rphast/inst/doc/vignette3.pdf
rphast/inst/doc/vignette1.R
rphast/inst/doc/vignette3.R
rphast/inst/doc/vignette4.pdf
rphast/inst/doc/vignette4.R
rphast/inst/doc/vignette1.pdf
rphast/inst/doc/vignette3.Rnw
rphast/configure.ac
rphast/tests
rphast/tests/msa.examples.R
rphast/tests/phyloP.examples.R
rphast/tests/optim.examples.R
rphast/tests/feat.examples.R
rphast/src
rphast/src/queues.h
rphast/src/hmm.c
rphast/src/tfbs.c
rphast/src/phylo_p_print.h
rphast/src/hashtable.h
rphast/src/prob_vector.h
rphast/src/phylo_p.h
rphast/src/simplex_grid.h
rphast/src/bed.h
rphast/src/matrix.c
rphast/src/bed.c
rphast/src/maf.c
rphast/src/hashtable.c
rphast/src/rph_category_map.c
rphast/src/list_of_lists.c
rphast/src/indel_mod.h
rphast/src/em.h
rphast/src/fit_column.h
rphast/src/phylo_hmm.c
rphast/src/sufficient_stats.c
rphast/src/tree_model.c
rphast/src/gap_patterns.c
rphast/src/rph_phastCons.c
rphast/src/fit_column.c
rphast/src/rph_hmm.c
rphast/src/subst_distrib.c
rphast/src/stacks.h
rphast/src/pbs_code.h
rphast/src/list_of_lists.h
rphast/src/subst_mods.h
rphast/src/misc.c
rphast/src/sufficient_stats.h
rphast/src/rph_trees.c
rphast/src/complex_vector.h
rphast/src/fit_em.c
rphast/src/rph_phylo_hmm.c
rphast/src/eigen.h
rphast/src/rph_subst_mods.c
rphast/src/bd_phylo_hmm.h
rphast/src/phylo_p.c
rphast/src/phast_cons.h
rphast/src/vector.c
rphast/src/rph_phyloP.c
rphast/src/tfbs.h
rphast/src/version
rphast/src/em.c
rphast/src/subst_mods.c
rphast/src/vector.h
rphast/src/local_alignment.c
rphast/src/multi_msa.h
rphast/src/numerical_opt.c
rphast/src/misc.h
rphast/src/pssm.h
rphast/src/rph_list_of_lists.c
rphast/src/memory_handler.c
rphast/src/markov_matrix.h
rphast/src/indel_history.c
rphast/src/indel_history.h
rphast/src/lists.c
rphast/src/bgc_hmm.h
rphast/src/gff.h
rphast/src/fit_em.h
rphast/src/motif.c
rphast/src/phylo_fit.h
rphast/src/prob_matrix.h
rphast/src/rph_bgc_hmm.c
rphast/src/eigen.c
rphast/src/phylo_p_print.c
rphast/src/markov_matrix.c
rphast/src/msa.h
rphast/src/rph_tfbs.c
rphast/src/tree_likelihoods.c
rphast/src/local_alignment.h
rphast/src/rph_tree_model.c
rphast/src/gap_patterns.h
rphast/src/subst_distrib.h
rphast/src/fit_feature.c
rphast/src/complex_vector.c
rphast/src/rph_gff.c
rphast/src/complex_matrix.c
rphast/src/fit_feature.h
rphast/src/category_map.h
rphast/src/Makevars.in
rphast/src/category_map.c
rphast/src/multi_msa.c
rphast/src/maf.h
rphast/src/wig.c
rphast/src/external_libs.h
rphast/src/complex_matrix.h
rphast/src/rph_util.c
rphast/src/gff.c
rphast/src/stringsplus.c
rphast/src/dgamma.c
rphast/src/wig.h
rphast/src/numerical_opt.h
rphast/src/rph_msa.c
rphast/src/bgc_hmm.c
rphast/src/tree_model.h
rphast/src/memory_handler.h
rphast/src/rph_util.h
rphast/src/complex.h
rphast/src/rph_init.c
rphast/src/maf_block.c
rphast/src/maf_block.h
rphast/src/Makevars.win
rphast/src/trees.h
rphast/src/hmm.h
rphast/src/ms.h
rphast/src/stringsplus.h
rphast/src/genepred.h
rphast/src/motif.h
rphast/src/puzzler.h
rphast/src/rph_wig.c
rphast/src/msa.c
rphast/src/genepred.c
rphast/src/phylo_fit.c
rphast/src/indel_mod.c
rphast/src/phylo_hmm.h
rphast/src/trees.c
rphast/src/phast_cons.c
rphast/src/rph_phyloFit.c
rphast/src/dgamma.h
rphast/src/lists.h
rphast/src/tree_likelihoods.h
rphast/src/prob_matrix.c
rphast/src/prob_vector.c
rphast/src/matrix.h
rphast/NAMESPACE
rphast/R
rphast/R/treeModel.R rphast/R/phastCons.R rphast/R/checkArgs.R rphast/R/rphast.R rphast/R/phyloP.R rphast/R/hmm.R rphast/R/plot.R rphast/R/feat.R rphast/R/optim.R rphast/R/phyloFit.R rphast/R/msa.R rphast/R/bgc.R rphast/R/zzz.R rphast/R/listOfLists.R rphast/R/trees.R
rphast/vignettes
rphast/vignettes/vignette1.Rnw
rphast/vignettes/vignette4.Rnw
rphast/vignettes/rphast.bib
rphast/vignettes/vignette3.Rnw
rphast/MD5
rphast/build
rphast/build/vignette.rds
rphast/DESCRIPTION
rphast/configure
rphast/ChangeLog
rphast/man
rphast/man/write.feat.Rd rphast/man/branchlength.tree.Rd rphast/man/from.pointer.msa.Rd rphast/man/apply.bgc.sel.Rd rphast/man/as.track.msa.Rd rphast/man/add.signals.feat.Rd rphast/man/tm.Rd rphast/man/ninf.msa.Rd rphast/man/phyloP.sph.Rd rphast/man/nrow.feat.Rd rphast/man/composition.feat.Rd rphast/man/extract.feature.msa.Rd rphast/man/optim.rphast.Rd rphast/man/copy.msa.Rd rphast/man/write.wig.Rd rphast/man/plot.gene.Rd rphast/man/ncol.feat.Rd rphast/man/write.msa.Rd rphast/man/ncol.msa.Rd rphast/man/register.rphast.Rd rphast/man/sample.msa.Rd rphast/man/get4d.msa.Rd rphast/man/translate.msa.Rd rphast/man/label.subtree.Rd rphast/man/subtree.Rd rphast/man/strip.gaps.msa.Rd rphast/man/as.pointer.msa.Rd rphast/man/copy.feat.Rd rphast/man/msa.Rd rphast/man/phyloFit.Rd rphast/man/classify.muts.bgc.Rd rphast/man/coverage.feat.Rd rphast/man/nrow.msa.Rd rphast/man/col.expected.subs.msa.Rd rphast/man/add.ls.mod.Rd rphast/man/mod.backgd.tm.Rd rphast/man/as.data.frame.feat.Rd rphast/man/is.subst.mod.tm.Rd rphast/man/postprob.msa.Rd rphast/man/as.list.tm.Rd rphast/man/pairwise.diff.msa.Rd rphast/man/flatten.feat.Rd rphast/man/summary.msa.Rd rphast/man/phyloP.Rd rphast/man/fix.start.stop.feat.Rd rphast/man/plot.msa.Rd rphast/man/tagval.feat.Rd rphast/man/read.msa.Rd rphast/man/sub.msa.Rd rphast/man/hmm.Rd rphast/man/alphabet.msa.Rd rphast/man/write.wig.feat.Rd rphast/man/rbind.feat.Rd rphast/man/summary.feat.Rd rphast/man/enrichment.feat.Rd rphast/man/write.hmm.Rd rphast/man/prune.tree.Rd rphast/man/read.wig.Rd rphast/man/as.pointer.feat.Rd rphast/man/total.expected.subs.msa.Rd rphast/man/complement.Rd rphast/man/unapply.bgc.sel.Rd rphast/man/range.track.Rd rphast/man/names.msa.Rd rphast/man/set.rate.matrix.tm.Rd rphast/man/write.tm.Rd rphast/man/print.tm.Rd rphast/man/phyloP.prior.Rd rphast/man/print.msa.Rd rphast/man/range.feat.Rd rphast/man/informative.regions.msa.Rd rphast/man/summary.tm.Rd rphast/man/bgc.informative.Rd rphast/man/dim.msa.Rd rphast/man/square-bracket-msa.Rd rphast/man/print.feat.Rd rphast/man/overlap.feat.Rd rphast/man/concat.msa.Rd rphast/man/likelihood.msa.Rd rphast/man/convert.coords.feat.Rd rphast/man/subst.mods.Rd rphast/man/read.hmm.Rd rphast/man/bgc.nucleotide.tests.Rd rphast/man/add.UTRs.feat.Rd rphast/man/depth.tree.Rd rphast/man/read.tm.Rd rphast/man/inverse.feat.Rd rphast/man/is.msa.Rd rphast/man/smooth.wig.Rd rphast/man/base.freq.msa.Rd rphast/man/is.tm.Rd rphast/man/sort.feat.Rd rphast/man/gc.content.msa.Rd rphast/man/add.introns.feat.Rd rphast/man/rename.tree.Rd rphast/man/plot.tm.Rd rphast/man/get.rate.matrix.params.tm.Rd rphast/man/codon.clean.msa.Rd rphast/man/read.newick.tree.Rd rphast/man/numnodes.tree.Rd rphast/man/print.phastBiasResult.Rd rphast/man/offset.msa.Rd rphast/man/score.hmm.Rd rphast/man/dim.feat.Rd rphast/man/as.track.wig.Rd rphast/man/reverse.complement.msa.Rd rphast/man/name.ancestors.Rd rphast/man/is.track.Rd rphast/man/reflect.phylo.hmm.Rd rphast/man/tagval.Rd rphast/man/plot.feat.Rd rphast/man/summary.tree.Rd rphast/man/state.freq.msa.Rd rphast/man/numleaf.tree.Rd rphast/man/split.feat.Rd rphast/man/phastCons.Rd rphast/man/phastBias.Rd rphast/man/as.track.feat.Rd rphast/man/density.feat.Rd rphast/man/square-bracket-assign-msa.Rd rphast/man/unique.feat.Rd rphast/man/read.feat.Rd rphast/man/label.branches.Rd rphast/man/freq3x4.msa.Rd rphast/man/setup.branch.site.tm.Rd rphast/man/nothanks.rphast.Rd rphast/man/split.by.feature.msa.Rd rphast/man/leafnames.tree.Rd rphast/man/is.format.msa.Rd rphast/man/from.pointer.feat.Rd rphast/man/is.ordered.msa.Rd rphast/man/fix.semicolon.tree.Rd rphast/man/plot.rate.matrix.Rd rphast/man/nstate.hmm.Rd rphast/man/feat.Rd rphast/man/guess.format.msa.Rd rphast/man/expected.subs.msa.Rd rphast/man/coord.range.msa.Rd rphast/man/hist.feat.Rd rphast/man/simulate.msa.Rd rphast/man/plot.lsmodel.tm.Rd rphast/man/rphast-package.Rd rphast/man/plot.track.Rd rphast/man/bgc.sel.factor.Rd rphast/man/rescale.tree.Rd
rphast/cleanup
rphast/LICENSE

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