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

Files in this package

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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