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
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.