[Biopython] clustalw align multiple sequences to reference.

[Daniel Jones]

Hi Biopython users,
I have a file with many (~50,000) 200 bp sequences, each of which I would
like to align to a fixed reference sequence. I *don't* care about aligning
all 50,000 sequences with each other; I only care about aligning each one
with the reference sequence. I can't figure out a way to do this without
generating 50,000 files, which seems like ridiculous unnecessary overhead.
It seems like ClustalW's interface is quite inflexible in demanding separate
input and output files for each alignment, but I don't have much experience
using it so maybe I'm completely missing something.

Incidentally, I'm not wedded to the idea of using ClustalW, so if there's an
alternate alignment program that would make this easier, I'd certainly be
open to trying it.

Thanks,
Daniel Jones