[Biopython] "Appending" to an MSA

[Peter Cock]

On Monday, July 29, 2013, Eric Ma wrote:

> Many apologies if this sounds like a dumb question, but I'm kinda stuck
> here. I've posted on StackOverflow and BioStars, but haven't received an
> answer, so I'm going to cross-post my question below.
>
>
Links? I don't see it here - maybe you didn't tag the question?
http://www.biostars.org/show/tag/biopython/

Here's the duplicate on SO:
http://stackoverflow.com/questions/17911075/multiple-sequence-alignment-appending-to-an-alignment


> I have a set of 520 influenza sequences for which I have already done
> multiple sequence alignment, and computed the pairwise identity matrix. If
> I'd like to add in another sequence, I have to re-align everything, and
> recompute the entire PWI matrix. Is there any program I can use to "append"
> this other sequence to the alignment, and only compute the PWI w.r.t. every
> other sequence?


I think some command line tools will do that, but it may give a
different answer to a fresh alignment - and therefore could be
a bad idea for many downstream analyses...

Are you hoping for advice for how to implement this yourself
in (bio)python?

Peter