A B C D E F G H I L M N O P R S T U W misc
rphast-package | R interface to PHAST software for comparative genomics |
add.alt.mod | Add a lineage-specific model... |
add.introns.feat | Add introns to features... |
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.sel.factor | BGC+selection factor... |
branchlength.tree | Get the total length of the edges of a tree... |
codon.clean.msa | Clean an alignment for codon analysis... |
col.expected.subs.msa | Obtain expected number of substitutions on each branch for each site... |
complement | complement |
composition.feat | Composition of features with respect to annotations... |
concat.msa | Concatenate msa objects... |
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... |
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 Format From Filename Extension |
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 |
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... |
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 |
overlap.feat | Feature overlap... |
pairwise.diff.msa | Get pairwise differences per site between sequences... |
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.altmodel.tm | Make a bubble plot of a lineage-specific transition matrix of a... |
plot.feat | Features plot |
plot.gene | Gene plot |
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.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 |
rename.tree | Tree Node Renaming |
rescale.tree | Scale a Tree or Subtree |
reverse.complement.msa | Reverse complement a multiple sequence alignment... |
rphast | R 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 parameters. |
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 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 |
[.msa | Extract, replace, reorder MSA... |