[Molecular-evolution] Re: Pairwise alignements versus multiple alignement for distance matrix

Kevin Karplus via mol-evol%40net.bio.net (by karplus from cheep.cse.ucsc.edu)
Tue Feb 27 16:28:53 EST 2007

On 2007-02-26, Ahmed Moustafa <ahmed from pobox.com> wrote:
> Dear All,
> Generally distance-based tree construction methods begin with multiple
> sequence alignment for the protein sequences and than measuring the
> distances between each two sequences in the alignment to fill in the
> distance matrix.
> 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.
> Thanks in advance!
> Ahmed

The distance matrix can be computed from pairwise alignments, but
computng n*(n-1)/2 pairwise alignments is often slower than
constructing a multiple sequence alignment (depending on the MSA
method) and the resulting distances are less accurate.

Kevin Karplus 	karplus from soe.ucsc.edu	http://www.soe.ucsc.edu/~karplus
Professor of Biomolecular Engineering, University of California, Santa Cruz
Undergraduate and Graduate Director, Bioinformatics
(Senior member, IEEE)	(Board of Directors & Chair of Education Committee, ISCB)
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