coord.range.msa

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

A character string identifying the reference sequence
(or NULL to use frame of reference of entire alignment)

refseq

Obtain the range of coordinates in a MSA objects

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.

coord.range.msa: Obtain the range of coordinates in a MSA objects

Description

Usage

Arguments

Value