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rphast (version 1.6.9)

Interface to 'PHAST' Software for Comparative Genomics

Description

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.

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Version

Install

install.packages('rphast')

Monthly Downloads

109

Version

1.6.9

License

BSD_3_clause + file LICENSE

Maintainer

Ritika Ramani

Last Published

February 11th, 2018

Functions in rphast (1.6.9)

add.UTRs.feat

Add UTRs to features
col.expected.subs.msa

Obtain expected number of substitutions on each branch for each site pattern and each substitution type
complement

complement
hmm

Create an rphast HMM object
depth.tree

Get the distance from a node to the root of a tree
informative.regions.msa

Get informative regions of an alignment
dim.feat

Feature dimensions
is.track

Is this a track?
label.branches

Label tree branches
likelihood.msa

MSA Likelihood
add.ls.mod

Add a lineage-specific model
add.signals.feat

Add start/stop codon, 3'/5' splice signals to features
as.track.feat

Create a features track
mod.backgd.tm

Adjust tree model background frequencies while maintaining reversibility
offset.msa

MSA Index Offset
composition.feat

Composition of features with respect to annotations
as.track.msa

Create an alignment track
as.data.frame.feat

Features to Data Frame
optim.rphast

Optimize using phast's optimization code
concat.msa

Concatenate msa objects
phyloP.prior

phyloP prior
expected.subs.msa

Obtain expected number of substitutions on each branch and site
as.list.tm

Tree Model to List
phyloP.sph

phyloP SPH
as.pointer.feat

Features To Pointer
as.pointer.msa

MSA To Pointer
print.feat

Printing a features Object
classify.muts.bgc

Count the number of mutations of each gBGC type on each branch
bgc.informative

Return features indicating regions informative for bgc
extract.feature.msa

Extract features from an MSA object
codon.clean.msa

Clean an alignment for codon analysis
bgc.nucleotide.tests

Do maximum likelihood analysis for gBGC and selection using nucleotide model
read.feat

Read a Feature File (GFF, BED, or GenePred)
print.msa

Printing MSA objects
copy.feat

Features copy
freq3x4.msa

Get codon frequencies based on 3x4 model
from.pointer.feat

Convert a features object from C memory (external pointer) to R memory
leafnames.tree

Get the names of a tree's leaf nodes
read.hmm

Read an HMM object from a file
copy.msa

MSA copy
apply.bgc.sel

Apply bgc+selection parameters to a matrix
label.subtree

Label subtree
alphabet.msa

MSA Alphabet
ncol.msa

MSA Sequence Length.
as.track.wig

Create a wig track
density.feat

Features kernel density
coverage.feat

Features coverage
ninf.msa

The number of informative columns in an alignment
reverse.complement.msa

Reverse complement a multiple sequence alignment
fix.start.stop.feat

Fix start and stop signals
summary.feat

Features Summary
rphast-package

Interface to 'PHAST' Software for Comparative Genomics
base.freq.msa

Get the frequencies of characters in an alignment
convert.coords.feat

Convert coordinates from one frame of reference to another
coord.range.msa

Obtain the range of coordinates in a MSA objects
flatten.feat

Combine adjacent features with the same "feature" field
fix.semicolon.tree

Add a semi-colon to end of tree string
summary.msa

MSA Summary
dim.msa

Returns the dimensions of an msa object as (# of species, # of columns)
feat

Features Objects
enrichment.feat

Enrichment of features with respect to annotation types
get.rate.matrix.params.tm

Get the parameters describing a rate matrix
get4d.msa

Extract fourfold degenerate sites from an MSA object
tagval

Extract value from tag-value formatted attributes
is.msa

Check an MSA object
is.ordered.msa

MSA is Ordered?
from.pointer.msa

MSA From Pointer
names.msa

MSA Sequence Names
gc.content.msa

Get the fraction of G's and C's in an alignment
guess.format.msa

MSA Guess Format
is.subst.mod.tm

Check Substitution Model Strings
tagval.feat

Extract value from tag-value formatted attribute in features object
is.tm

Tree Models
hist.feat

plot histogram of feature lengths
ncol.feat

Number of Columns in Features
nrow.msa

MSA Number of Sequences
phastBias

phastBias
inverse.feat

Get inverse features
msa

MSA Objects
phastCons

Produce conservation scores and identify conserved elements, given a multiple alignment and a phylo-HMM.
is.format.msa

Check an MSA Format String
name.ancestors

Name Ancestral Nodes
nothanks.rphast

Stop rphast registration reminders
nrow.feat

Number of Features
plot.rate.matrix

Make a bubble plot of a transition matrix
numleaf.tree

Number of leaves in a Tree
overlap.feat

Feature overlap
numnodes.tree

Number of Nodes in a Tree
pairwise.diff.msa

Get pairwise differences per site between sequences
plot.tm

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

Fit a Phylogenetic model to an alignment...
phyloP

phyloP (basewise or by feature)
prune.tree

Prune a Tree
nstate.hmm

HMM number of states
plot.track

Make browser-like plot in rphast
plot.lsmodel.tm

Make a bubble plot of a lineage-specific transition matrix of a tree model.
postprob.msa

Obtain posterior probilities of every state at every node
rename.tree

Tree Node Renaming
range.feat

Features range
plot.msa

Plot an alignment
read.wig

Read a wig file
split.by.feature.msa

Split an MSA by feature
sort.feat

Sort a GFF
subst.mods

List PHAST Substitution Models
read.tm

Read a Tree Model
subtree

Subtree
plot.feat

Features plot
translate.msa

Get amino acid sequences from an alignment
plot.gene

Gene plot
print.phastBiasResult

Pretty-print the phastBias result list without spilling giant matrices onto the screen
range.track

Get the coordinate range of a list of RPHAST results
rescale.tree

Scale a Tree or Subtree
print.tm

Printing Tree Models
read.msa

Reading an MSA Object
rbind.feat

concatenate feature objects
unapply.bgc.sel

Unapply bgc+selection parameters from a matrix
read.newick.tree

Read a Newick Tree from a File
simulate.msa

Simulate a MSA given a tree model and HMM.
smooth.wig

Smooth a wig plot in rphast
[<-.msa

Replace subsets of an alignment
write.hmm

Write an HMM object to a file
split.feat

Split features by length
sample.msa

Sample columns from an MSA
reflect.phylo.hmm

Reflect a phylo-hmm across a strand
tm

Tree Models
write.msa

Writing MSA Objects to Files
total.expected.subs.msa

Obtain expected number of substitutions of each type on each branch
register.rphast

Register RPHAST
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
score.hmm

Score an alignment using a general phylo-HMM
strip.gaps.msa

MSA Strip Gaps
[.msa

Extract, replace, reorder MSA
write.tm

Wrting Tree Models
sub.msa

MSA Subset
write.wig

Writing a wig file
unique.feat

Remove overlapping genes
state.freq.msa

Get the observed frequencies of states in an alignment
summary.tree

Get a summary of a Newick-formatted tree, edge lengths, node names, etc
summary.tm

Tree Model Summary
write.feat

Writing a features Object
write.wig.feat

Write a features object in fixedStep wig format
add.introns.feat

Add introns to features
bgc.sel.factor

BGC+selection factor
branchlength.tree

Get the total length of the edges of a tree