# Interface to PHAST Software for Comparative Genomics

## Documentation for package ‘rphast’ version 1.6.5

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D E F G H I L M N O P R S T U W misc

rphast-package | Interface to PHAST Software for Comparative Genomics

## -- A --

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

## -- B --

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

## -- C --

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

## -- D --

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)

## -- E --

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

## -- F --

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

## -- G --

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

## -- H --

hist.feat | plot histogram of feature lengths
hmm | Create an rphast HMM object

## -- I --

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?

## -- L --

label.branches | Label tree branches
label.subtree | Label subtree
leafnames.tree | Get the names of a tree's leaf nodes
likelihood.msa | MSA Likelihood

## -- M --

mod.backgd.tm | Adjust tree model background frequencies while maintaining reversibility
msa | MSA Objects

## -- N --

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

## -- O --

offset.msa | MSA Index Offset
optim.rphast | Optimize using phast's optimization code
overlap.feat | Feature overlap

## -- P --

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

## -- R --

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 | Interface to PHAST Software for Comparative Genomics

## -- S --

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

## -- T --

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

## -- U --

unapply.bgc.sel | Unapply bgc+selection parameters from a matrix
unique.feat | Remove overlapping genes

## -- W --

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

## -- misc --

[.msa | Extract, replace, reorder MSA
[<-.msa | Replace subsets of an alignment