msa2mat: Convert alignment to matrix

In microseq: Basic Biological Sequence Handling

Convert alignment to matrix

Description

Converts a FASTA formatted multiple alignment to a matrix.

Usage

msa2mat(msa)

Arguments

msa	A fasta object with a multiple alignment, see msalign'.

Details

This function converts the fasta object msa, containing a multiple alignment, to a matrix. This means each position in the alignment is a column in the matrix, and the content of the ‘⁠Header⁠’ column of msa is used as rownames of theh matrix.

Such a matrix is useful for conversion to a DNAbin object that is used by the ape package for re-constructing phylogenetic trees.

Value

A matrix where each row is a vector of aligned bases/amino acids.

Author(s)

Lars Snipen.

See Also

msalign, readFasta.

Examples

msa.file <- file.path(path.package("microseq"),"extdata", "small.msa")
msa <- readFasta(msa.file)
msa.mat <- msa2mat(msa)  # to use with ape::as.DNAbin(msa.mat)

microseq documentation built on Aug. 21, 2023, 5:10 p.m.