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