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

Ahmed Moustafa via bio-soft%40net.bio.net (by ahmed from pobox.com)
Wed Feb 28 18:58:26 EST 2007

On 2/28/2007 7:45 AM, Kevin Karplus wrote:
> On 2007-02-28, Ahmed Moustafa <ahmed from pobox.com> wrote:
>> But MSA methods perform the pairwise alignments anyway as an initial 
>> step to cluster or join the sequences in the multiple alignment. Also 
>> MSA methods are approximation while pairwise alignment methods computes 
>> the optimal alignments, so they give absolute values representing the 
>> relatednesses (or distances) between the sequences.
> Only very slow (and ancient) MSA methods start with full pairwise alignments.
> Multiple sequence alignments are better alignments than independent
> pairwise ones, because they can better disambiguate alignments where
> the signal is weak.  The evolutionary distance measures from MSAs are
> crude, but the ones from pairwise alignments alignments are often even
> cruder.

Regardless of the evolutionary distance, my guess is that for closely 
related sequences, pairwise alignments would be more sensitive than 
multiple alignment and resolve the relationships between the sequences 
and cluster them accurately.

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