Convert alignment to matrix
Converts a FASTA formatted multiple alignment to a matrix.
msa2mat(msa)
msa |
A fasta object with a multiple alignment, see |
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.
A matrix where each row is a vector of aligned bases/amino acids.
Lars Snipen.
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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.