rphast: Interface to PHAST Software for Comparative Genomics

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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.

Author
Melissa Hubisz, Katherine Pollard, and Adam Siepel
Date of publication
2016-08-16 00:25:52
Maintainer
Melissa Hubisz <mjhubisz@cornell.edu>
License
BSD_3_clause + file LICENSE
Version
1.6.5
URLs

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