rphast: Interface to PHAST Software for Comparative Genomics
Version 1.6.5

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.

Browse man pages Browse package API and functions Browse package files

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
URL http://compgen.cshl.edu/rphast
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("rphast")

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

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

Files

inst
inst/examples
inst/examples/summary-tree.R
inst/examples/likelihood-msa.R
inst/examples/write-wig.R
inst/examples/sub-msa.R
inst/examples/phastCons.R
inst/examples/col-expected-subs-msa.R
inst/examples/score-hmm.R
inst/examples/as-data-frame-feat.R
inst/examples/split-by-feature-msa.R
inst/examples/as-pointer-feat.R
inst/examples/summary-tm.R
inst/examples/read-msa.R
inst/examples/subtree.R
inst/examples/reflect-phylo-hmm.R
inst/examples/convert-coords-feat.R
inst/examples/write-msa.R
inst/examples/is-subst-mod-tm.R
inst/examples/phyloP.R
inst/examples/subst-mods.R
inst/examples/plot-msa.R
inst/examples/hmm.R
inst/examples/numnodes-tree.R
inst/examples/as-pointer-msa.R
inst/examples/nrow-feat.R
inst/examples/prune-tree.R
inst/examples/offset-msa.R
inst/examples/fix-semicolon-tree.R
inst/examples/feat.R
inst/examples/names-msa.R
inst/examples/coverage-feat.R
inst/examples/plot-lsmodel-tm.R
inst/examples/postprob-msa.R
inst/examples/square-bracket-assign-msa.R
inst/examples/informative-regions-msa.R
inst/examples/fix-start-stop-feat.R
inst/examples/expected-subs-msa.R
inst/examples/mod-backgd-tm.R
inst/examples/write-hmm.R
inst/examples/write-wig-feat.R
inst/examples/strip-gaps-msa.R
inst/examples/add-introns-feat.R
inst/examples/get4d-msa.R
inst/examples/sample-msa.R
inst/examples/phyloP-prior.R
inst/examples/square-bracket-msa.R
inst/examples/tm.R
inst/examples/print-msa.R
inst/examples/simulate-msa.R
inst/examples/ncol-msa.R
inst/examples/label-branches.R
inst/examples/translate-msa.R
inst/examples/as-track-feat.R
inst/examples/read-feat.R
inst/examples/add-signals-feat.R
inst/examples/nrow-msa.R
inst/examples/summary-msa.R
inst/examples/is-ordered-msa.R
inst/examples/read-hmm.R
inst/examples/read-newick-tree.R
inst/examples/name-ancestors.R
inst/examples/alphabet-msa.R
inst/examples/rescale-tree.R
inst/examples/dim-feat.R
inst/examples/print-tm.R
inst/examples/phyloFit.R
inst/examples/add-UTRs-feat.R
inst/examples/write-feat.R
inst/examples/plot-tm.R
inst/examples/rename-tree.R
inst/examples/msa.R
inst/examples/as-list-tm.R
inst/examples/plot-feat.R
inst/examples/plot-gene.R
inst/examples/read-tm.R
inst/examples/total-expected-subs-msa.R
inst/examples/from-pointer-msa.R
inst/examples/overlap-feat.R
inst/examples/label-subtree.R
inst/examples/summary-feat.R
inst/examples/guess-format-msa.R
inst/examples/ncol-feat.R
inst/examples/write-tm.R
inst/examples/tagval.R
inst/examples/is-format-msa.R
inst/examples/tagval-feat.R
inst/extdata
inst/extdata/NRSF.zip
inst/extdata/examples.zip
inst/doc
inst/doc/vignette1.Rnw
inst/doc/vignette4.Rnw
inst/doc/vignette3.pdf
inst/doc/vignette1.R
inst/doc/vignette3.R
inst/doc/vignette4.pdf
inst/doc/vignette4.R
inst/doc/vignette1.pdf
inst/doc/vignette3.Rnw
configure.ac
tests
tests/msa.examples.R
tests/phyloP.examples.R
tests/optim.examples.R
tests/feat.examples.R
src
src/queues.h
src/hmm.c
src/tfbs.c
src/phylo_p_print.h
src/hashtable.h
src/prob_vector.h
src/phylo_p.h
src/simplex_grid.h
src/bed.h
src/matrix.c
src/bed.c
src/maf.c
src/hashtable.c
src/rph_category_map.c
src/list_of_lists.c
src/indel_mod.h
src/em.h
src/fit_column.h
src/phylo_hmm.c
src/sufficient_stats.c
src/tree_model.c
src/gap_patterns.c
src/rph_phastCons.c
src/fit_column.c
src/rph_hmm.c
src/subst_distrib.c
src/stacks.h
src/pbs_code.h
src/list_of_lists.h
src/subst_mods.h
src/misc.c
src/sufficient_stats.h
src/rph_trees.c
src/complex_vector.h
src/fit_em.c
src/rph_phylo_hmm.c
src/eigen.h
src/rph_subst_mods.c
src/bd_phylo_hmm.h
src/phylo_p.c
src/phast_cons.h
src/vector.c
src/rph_phyloP.c
src/tfbs.h
src/version
src/em.c
src/subst_mods.c
src/vector.h
src/local_alignment.c
src/multi_msa.h
src/numerical_opt.c
src/misc.h
src/pssm.h
src/rph_list_of_lists.c
src/memory_handler.c
src/markov_matrix.h
src/indel_history.c
src/indel_history.h
src/lists.c
src/bgc_hmm.h
src/gff.h
src/fit_em.h
src/motif.c
src/phylo_fit.h
src/prob_matrix.h
src/rph_bgc_hmm.c
src/eigen.c
src/phylo_p_print.c
src/markov_matrix.c
src/msa.h
src/rph_tfbs.c
src/tree_likelihoods.c
src/local_alignment.h
src/rph_tree_model.c
src/gap_patterns.h
src/subst_distrib.h
src/fit_feature.c
src/complex_vector.c
src/rph_gff.c
src/complex_matrix.c
src/fit_feature.h
src/category_map.h
src/Makevars.in
src/category_map.c
src/multi_msa.c
src/maf.h
src/wig.c
src/external_libs.h
src/complex_matrix.h
src/rph_util.c
src/gff.c
src/stringsplus.c
src/dgamma.c
src/wig.h
src/numerical_opt.h
src/rph_msa.c
src/bgc_hmm.c
src/tree_model.h
src/memory_handler.h
src/rph_util.h
src/complex.h
src/rph_init.c
src/maf_block.c
src/maf_block.h
src/Makevars.win
src/trees.h
src/hmm.h
src/ms.h
src/stringsplus.h
src/genepred.h
src/motif.h
src/puzzler.h
src/rph_wig.c
src/msa.c
src/genepred.c
src/phylo_fit.c
src/indel_mod.c
src/phylo_hmm.h
src/trees.c
src/phast_cons.c
src/rph_phyloFit.c
src/dgamma.h
src/lists.h
src/tree_likelihoods.h
src/prob_matrix.c
src/prob_vector.c
src/matrix.h
NAMESPACE
R
R/treeModel.R
R/phastCons.R
R/checkArgs.R
R/rphast.R
R/phyloP.R
R/hmm.R
R/plot.R
R/feat.R
R/optim.R
R/phyloFit.R
R/msa.R
R/bgc.R
R/zzz.R
R/listOfLists.R
R/trees.R
vignettes
vignettes/vignette1.Rnw
vignettes/vignette4.Rnw
vignettes/rphast.bib
vignettes/vignette3.Rnw
MD5
build
build/vignette.rds
DESCRIPTION
configure
ChangeLog
man
man/write.feat.Rd
man/branchlength.tree.Rd
man/from.pointer.msa.Rd
man/apply.bgc.sel.Rd
man/as.track.msa.Rd
man/add.signals.feat.Rd
man/tm.Rd
man/ninf.msa.Rd
man/phyloP.sph.Rd
man/nrow.feat.Rd
man/composition.feat.Rd
man/extract.feature.msa.Rd
man/optim.rphast.Rd
man/copy.msa.Rd
man/write.wig.Rd
man/plot.gene.Rd
man/ncol.feat.Rd
man/write.msa.Rd
man/ncol.msa.Rd
man/register.rphast.Rd
man/sample.msa.Rd
man/get4d.msa.Rd
man/translate.msa.Rd
man/label.subtree.Rd
man/subtree.Rd
man/strip.gaps.msa.Rd
man/as.pointer.msa.Rd
man/copy.feat.Rd
man/msa.Rd
man/phyloFit.Rd
man/classify.muts.bgc.Rd
man/coverage.feat.Rd
man/nrow.msa.Rd
man/col.expected.subs.msa.Rd
man/add.ls.mod.Rd
man/mod.backgd.tm.Rd
man/as.data.frame.feat.Rd
man/is.subst.mod.tm.Rd
man/postprob.msa.Rd
man/as.list.tm.Rd
man/pairwise.diff.msa.Rd
man/flatten.feat.Rd
man/summary.msa.Rd
man/phyloP.Rd
man/fix.start.stop.feat.Rd
man/plot.msa.Rd
man/tagval.feat.Rd
man/read.msa.Rd
man/sub.msa.Rd
man/hmm.Rd
man/alphabet.msa.Rd
man/write.wig.feat.Rd
man/rbind.feat.Rd
man/summary.feat.Rd
man/enrichment.feat.Rd
man/write.hmm.Rd
man/prune.tree.Rd
man/read.wig.Rd
man/as.pointer.feat.Rd
man/total.expected.subs.msa.Rd
man/complement.Rd
man/unapply.bgc.sel.Rd
man/range.track.Rd
man/names.msa.Rd
man/set.rate.matrix.tm.Rd
man/write.tm.Rd
man/print.tm.Rd
man/phyloP.prior.Rd
man/print.msa.Rd
man/range.feat.Rd
man/informative.regions.msa.Rd
man/summary.tm.Rd
man/bgc.informative.Rd
man/dim.msa.Rd
man/square-bracket-msa.Rd
man/print.feat.Rd
man/overlap.feat.Rd
man/concat.msa.Rd
man/likelihood.msa.Rd
man/convert.coords.feat.Rd
man/subst.mods.Rd
man/read.hmm.Rd
man/bgc.nucleotide.tests.Rd
man/add.UTRs.feat.Rd
man/depth.tree.Rd
man/read.tm.Rd
man/inverse.feat.Rd
man/is.msa.Rd
man/smooth.wig.Rd
man/base.freq.msa.Rd
man/is.tm.Rd
man/sort.feat.Rd
man/gc.content.msa.Rd
man/add.introns.feat.Rd
man/rename.tree.Rd
man/plot.tm.Rd
man/get.rate.matrix.params.tm.Rd
man/codon.clean.msa.Rd
man/read.newick.tree.Rd
man/numnodes.tree.Rd
man/print.phastBiasResult.Rd
man/offset.msa.Rd
man/score.hmm.Rd
man/dim.feat.Rd
man/as.track.wig.Rd
man/reverse.complement.msa.Rd
man/name.ancestors.Rd
man/is.track.Rd
man/reflect.phylo.hmm.Rd
man/tagval.Rd
man/plot.feat.Rd
man/summary.tree.Rd
man/state.freq.msa.Rd
man/numleaf.tree.Rd
man/split.feat.Rd
man/phastCons.Rd
man/phastBias.Rd
man/as.track.feat.Rd
man/density.feat.Rd
man/square-bracket-assign-msa.Rd
man/unique.feat.Rd
man/read.feat.Rd
man/label.branches.Rd
man/freq3x4.msa.Rd
man/setup.branch.site.tm.Rd
man/nothanks.rphast.Rd
man/split.by.feature.msa.Rd
man/leafnames.tree.Rd
man/is.format.msa.Rd
man/from.pointer.feat.Rd
man/is.ordered.msa.Rd
man/fix.semicolon.tree.Rd
man/plot.rate.matrix.Rd
man/nstate.hmm.Rd
man/feat.Rd
man/guess.format.msa.Rd
man/expected.subs.msa.Rd
man/coord.range.msa.Rd
man/hist.feat.Rd
man/simulate.msa.Rd
man/plot.lsmodel.tm.Rd
man/rphast-package.Rd
man/plot.track.Rd
man/bgc.sel.factor.Rd
man/rescale.tree.Rd
cleanup
LICENSE
rphast documentation built on May 20, 2017, 2:56 a.m.