[Bio-software] Re: Pairwise alignements versus multiple alignement for distance matrix

[Bastien Chevreux]

Ahmed Moustafa wrote:
> [...]
> My question is why not rather than performing the multiple sequence
> alignment, simply use pairwise alignments scores to fill in the
> distance matrix and from there to construct and infer the tree.

I think that clustalw works like this, doesn't it?

This is because there are no real good multiple alignment sequences that can
tackle more than a few dozen sequences at once without an explosion of time
and memory requirements. (Stoye et al have some nice publications on this).

Regards,
  Bastien