Writes a multiple sequence alignment (MSA) object to a file in one of several formats.
write.msa(x, file=NULL,
format=ifelse((f <- guess.format.msa(file, method="extension"))=="UNKNOWN", "FASTA", f),
pretty.print=FALSE)an object of class msa
File to write (will be overwritten). If NULL, output goes to terminal.
format to write MSA object. Valid values are "FASTA", "PHYLIP", "MPM", or "SS".
Whether to pretty-print alignment (turning bases which match the first base in the same column to ".").