rphast (version 1.0)

write.msa: Writing MSA Objects to Files

Description

Writes a multiple sequence alignment (MSA) object to a file in one of several formats.

Usage

write.msa(msa, filename=NULL, format=c(guess.format.msa(filename),
    "FASTA")[1], pretty.print=FALSE)

Arguments

msa

an object of class msa

filename

File to write (will be overwritten). If NULL, output goes to terminal.

format

format to write MSA object. Valid values are "FASTA", "PHYLIP", "MPM", or "SS".

pretty.print

Whether to pretty-print alignment (turning bases which match the first base in the same column to ".").

Examples

m <- msa(seqs=c("ACGTAT", "AGGTAA", "AGGTAG"),
         names=c("human", "mouse", "rat"))
write.msa(m, "foo.ss")
write.msa(m, "foo.fa", pretty.print=TRUE)
write.msa(m, NULL, format="PHYLIP", pretty.print=TRUE)

#clean up
unlink("foo.ss")
unlink("foo.fa")