gc.content.msa

An object of type <code>msa</code>

A vector of character strings identifying the sequence(s)
to use in the base frequency tabulation. If <code>NULL</code>, use all
sequences.

If <code>FALSE</code>, count missing data in the
denominator.

ignore.missing

If <code>TRUE</code>, count gaps in the denominator.

ignore.gaps

Get the fraction of G's and C's in an alignment

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.

gc.content.msa: Get the fraction of G's and C's in an alignment

Description

Usage

Arguments

Value