[Biopython] MUSCLE for alignment

林行众 linxzh1989 at gmail.com
Sat Apr 6 02:53:49 UTC 2013


Hi all !
I have a seqdump.fasta file:
>lcl|24977
TGAGAAAGACTTGAGAGGACA

>lcl|24977:8-21
GAGATGACTTAGAGGACA

I want to use a wrapper for Muscle in Biopython to align the two seq.
the alignment result will put into a existing fasta file.

>>>from Bio.Align.Applications import MuscleCommandline
>>>mcline = MuscleCommandline(input='seqdump.fasta',out='result.fasta')

But i can not find anything in the result.fasta after i run the command.
Do i have any missing to get the result?

regards
Lin



More information about the Biopython mailing list