def align(self, out_path=None):
if out_path is None: out_path = self.prefix_path + '<STR_LIT>'<EOL>sh.muscle38("<STR_LIT>", self.path, "<STR_LIT>", out_path)<EOL>return AlignedFASTA(out_path)<EOL>
We align the sequences in the fasta file with muscle.