Add UTRs to features
Obtain expected number of substitutions on each branch for each site pattern and each substitution type
complement
Create an rphast HMM object
Get the distance from a node to the root of a tree
Get informative regions of an alignment
Feature dimensions
Is this a track?
Label tree branches
MSA Likelihood
Add a lineage-specific model
Add start/stop codon, 3'/5' splice signals to features
Create a features track
Adjust tree model background frequencies while maintaining reversibility
MSA Index Offset
Composition of features with respect to annotations
Create an alignment track
Features to Data Frame
Optimize using phast's optimization code
Concatenate msa objects
phyloP prior
Obtain expected number of substitutions on each branch and site
Tree Model to List
phyloP SPH
Features To Pointer
MSA To Pointer
Printing a features Object
Count the number of mutations of each gBGC type on each branch
Return features indicating regions informative for bgc
Extract features from an MSA object
Clean an alignment for codon analysis
Do maximum likelihood analysis for gBGC and selection using nucleotide model
Read a Feature File (GFF, BED, or GenePred)
Printing MSA objects
Features copy
Get codon frequencies based on 3x4 model
Convert a features object from C memory (external pointer) to R memory
Get the names of a tree's leaf nodes
Read an HMM object from a file
MSA copy
Apply bgc+selection parameters to a matrix
Label subtree
MSA Alphabet
MSA Sequence Length.
Create a wig track
Features kernel density
Features coverage
The number of informative columns in an alignment
Reverse complement a multiple sequence alignment
Fix start and stop signals
Features Summary
Interface to 'PHAST' Software for Comparative Genomics
Get the frequencies of characters in an alignment
Convert coordinates from one frame of reference to another
Obtain the range of coordinates in a MSA objects
Combine adjacent features with the same "feature" field
Add a semi-colon to end of tree string
MSA Summary
Returns the dimensions of an msa object as (# of species, # of columns)
Features Objects
Enrichment of features with respect to annotation types
get.rate.matrix.params.tm
Get the parameters describing a rate matrix
Extract fourfold degenerate sites from an MSA object
Extract value from tag-value formatted attributes
Check an MSA object
MSA is Ordered?
MSA From Pointer
MSA Sequence Names
Get the fraction of G's and C's in an alignment
MSA Guess Format
Check Substitution Model Strings
Extract value from tag-value formatted attribute in features object
Tree Models
plot histogram of feature lengths
Number of Columns in Features
MSA Number of Sequences
phastBias
Get inverse features
MSA Objects
Produce conservation scores and identify conserved elements,
given a multiple alignment and a phylo-HMM.
Check an MSA Format String
Name Ancestral Nodes
Stop rphast registration reminders
Number of Features
Make a bubble plot of a transition matrix
Number of leaves in a Tree
Feature overlap
Number of Nodes in a Tree
Get pairwise differences per site between sequences
Make a bubble plot of the transition matrix for a tree model.
Fit a Phylogenetic model to an alignment...
phyloP (basewise or by feature)
Prune a Tree
HMM number of states
Make browser-like plot in rphast
Make a bubble plot of a lineage-specific transition matrix of a
tree model.
Obtain posterior probilities of every state at every node
Tree Node Renaming
Features range
Plot an alignment
Read a wig file
Split an MSA by feature
Sort a GFF
List PHAST Substitution Models
Read a Tree Model
Subtree
Features plot
Get amino acid sequences from an alignment
Gene plot
Pretty-print the phastBias result list without spilling giant matrices onto the screen
Get the coordinate range of a list of RPHAST results
Scale a Tree or Subtree
Printing Tree Models
Reading an MSA Object
concatenate feature objects
Unapply bgc+selection parameters from a matrix
Read a Newick Tree from a File
Simulate a MSA given a tree model and HMM.
Smooth a wig plot in rphast
Replace subsets of an alignment
Write an HMM object to a file
Split features by length
Sample columns from an MSA
Reflect a phylo-hmm across a strand
Tree Models
Writing MSA Objects to Files
Obtain expected number of substitutions of each type on each branch
Register RPHAST
Set the rate matrix of a tree model using model-specific parameters.
Set up a tree model for branch site selection analysis
Score an alignment using a general phylo-HMM
MSA Strip Gaps
Extract, replace, reorder MSA
Wrting Tree Models
MSA Subset
Writing a wig file
Remove overlapping genes
Get the observed frequencies of states in an alignment
Get a summary of a Newick-formatted tree, edge lengths, node names, etc
Tree Model Summary
Writing a features Object
Write a features object in fixedStep wig format
Add introns to features
BGC+selection factor
Get the total length of the edges of a tree