[Biopython] "Appending" to an MSA

[Eric Ma]

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.


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?

A simple example would be as follows. I have a 2x2 alignment, with the
following scores.

     SeqA SeqBSeqA 1.00 0.98SeqB 0.98 1.00

 Without re-running a full alignment, but only running "SeqC" against all
the other sequences, I'd like to get the following matrix:

     SeqA SeqB SeqCSeqA 1.00 0.98 0.99SeqB 0.98 1.00 0.97SeqC 0.99 0.97 1.00

 I am using the BioPython package, and Python is my preferred language, but
I'm okay with Java if need be too.

Does anybody have any idea whether this might be able to be done?
Cheers,
Eric
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