On 2/27/2007 3:28 PM, Kevin Karplus wrote:
> 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!
>> 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.
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.