rphast-package: Interface to 'PHAST' Software for Comparative Genomics
In rphast: Interface to 'PHAST' Software for Comparative Genomics

Description Details Author(s)

Provides an R interface to the 'PHAST'(<http://compgen.cshl.edu/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.

Copyright:	All code is Copyright (c) 2002-2018 University
	of California, Cornell University, Cold Spring Harbor Laboratory.
Package:	rphast
License:	BSD_3_clause + file LICENSE
Version:	1.6.9
URL:	http://compgen.cshl.edu/rphast
Date:	2018-01-30
Imports:	methods
Depends:
	stats
Suggests:
	ape,
	seqLogo
Collate:
	'bgc.R'
	'checkArgs.R'
	'feat.R'
	'hmm.R'
	'listOfLists.R'
	'msa.R'
	'optim.R'
	'phastCons.R'
	'phyloFit.R'
	'phyloP.R'
	'plot.R'
	'rphast.R'
	'treeModel.R'
	'trees.R'
	'zzz.R'
RoxygenNote:	5.0.1
Built:	R 3.1.2; x86_64-unknown-linux-gnu; 2018-01-30 15:53:11 UTC; unix

Index:

[.msa                   Extract, replace, reorder MSA
[<-.msa                 Replace subsets of an alignment
add.UTRs.feat           Add UTRs to features
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
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 nucleotide model
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 branch
codon.clean.msa         Clean an alignment for codon analysis
col.expected.subs.msa   Obtain expected number of substitutions on each
                        branch for each site pattern and each
                        substitution type
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, # of columns)
enrichment.feat         Enrichment of features with respect to
                        annotation types
expected.subs.msa       Obtain expected number of substitutions on each
                        branch and site
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 R memory
from.pointer.msa        MSA From Pointer
gc.content.msa          Get the fraction of G's and C's in an alignment
get.rate.matrix.params.tm
                        Get the parameters describing a rate matrix
get4d.msa               Extract fourfold degenerate sites from an MSA
                        object
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 reversibility
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, given a multiple alignment
                        and a phylo-HMM.
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 a tree model.
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 matrices onto the screen
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
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 parameters.
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
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 names, etc
tagval                  Extract value from tag-value formatted
                        attributes
tagval.feat             Extract value from tag-value formatted
                        attribute in features object
tm                      Tree Models
total.expected.subs.msa
                        Obtain expected number of substitutions of each
                        type on each branch
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