concat.msa

A list of MSA objects to concatenate together.

msas

If FALSE, disregard the order of columns in the combined
MSA.

ordered

(Advanced use only, for very large MSA objects) If
TRUE, return object will be a pointer to an object stored in C.

pointer.only

If the MSAs do not contain the same set of sequences, the sequences
will be added to each MSA and filled with missing data. The order
of sequences is taken from the first MSA, and sequences are added to
this as necessary.

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.

concat.msa: Concatenate msa objects

Description

Usage

Arguments

Value