def clustal_to_phylip(src,dest=None): import os from Bio.AlignIO.ClustalIO import ClustalIterator from Bio.AlignIO.PhylipIO import PhylipWriter if dest==None: dest = src head,tail = os.path.split(dest) _dest = os.path.join(head,"."+tail) with open(src) as i: alignments = list(ClustalIterator(i)) with open(_dest,"w") as f: writer = PhylipWriter(f) writer.write_file(alignments) os.rename(_dest,dest) return dest