state.freq.msa

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

align

An object of type <code>tm</code> representing a tree model.

Get the observed frequencies of states 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.

state.freq.msa: Get the observed frequencies of states in an alignment

Description

Usage

Arguments

Value