title: Multiple sequence alignment - appending to an alignment
body: <p>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?</p>
  
  <p>A simple example would be as follows. I have a 2x2 alignment, with the following scores.</p>
  
  <pre><code>     SeqA SeqB
  SeqA 1.00 0.98
  SeqB 0.98 1.00
  </code></pre>
  
  <p>Without re-running a full alignment, but only running "SeqC" against all the other sequences, I'd like to get the following matrix:</p>
  
  <pre><code>     SeqA SeqB SeqC
  SeqA 1.00 0.98 0.99
  SeqB 0.98 1.00 0.97
  SeqC 0.99 0.97 1.00
  </code></pre>
  
  <p>I am using the BioPython package, and Python is my preferred language, but I'm okay with Java if need be too.</p>
  
  <p>[I'll disclaim here that I'm cross-posting from BioStars, just in case there's experts here that aren't on BioStars. The BioStars post is: <a href="http://www.biostars.org/p/77607/" rel="nofollow">http://www.biostars.org/p/77607/</a>, but it has the exact same content.]</p>