extract.feature.msa

An object of type <code>features</code> denoting the regions
of the alignment to extract.

features

If <code>TRUE</code>, then some elements of features must have type "CDS", and only
fourfold-degenerate sites will be extracted.

do4d

If <code>TRUE</code>, return only a pointer to an object
stored in C (useful for large alignments; advanced use only)

pointer.only

Returns the subset of the MSA which appears in the features object.

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.

extract.feature.msa: Extract features from an MSA object

Description

Usage

Arguments

Value

See Also