How to write relaxed AND sequential Phylip format using AlignIO?
Hi,
I want to convert alignments in fasta-format to phylip format, and I need to use phylip relaxed unless my taxon-names would be identical. I would also prefer to have non-interleaved phylip format, but "phylip-sequential" shortens the names.
Here's my code:
from Bio import SeqIO
from Bio import AlignIO
from Bio.Alphabet import IUPAC, Gapped
alignment = AlignIO.read(open("test.fas"), "fasta", alphabet=Gapped(IUPAC.protein))
g = open("test.phy", "w")
g.write (alignment.format("phylip-relaxed"))
1 answer
You can use this tool http://bit.ly/1utdbFg to convert FASTA format to a relaxed PHYLIP format :)
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