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

Charles Plessy via bio-soft%40net.bio.net (by charles-news-nospam from plessy.org)
Thu Mar 1 20:50:30 EST 2007


Kevin Karplus a icrit :
> On 2007-02-27, Bastien Chevreux <bach from chevreux.org> wrote:
>> 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).
> 
> Actually there are some decent multiple sequence alignment algorithms
> that don't explode.  MUSCLE does fairly well up to a few thousand
> sequences and HMM-based methods (though not quite as good at multiple
> sequence alignments) are linear in the number of sequences and do
> fairly well up to tens of thousands of sequences.
> 
> MUSCLE does have an O(n^2) component, but it is a very fast
> approximate distance measure used to build a guide tree for
> progressive alignment.  The distance measure is then computed using
> the resulting MSA and the progressive alignment redone.
> See http://www.drive5.com/muscle/ for more info.

Dear all,

There is also Kalign which is really fast.

I would like to thake the opportunity of this thread to advertise the 
work we do in the Debian-Med project to make multiple alignment software 
easily available. If you have acces to a machine running Debian 
GNU/Linux, you can check on this page what programs are available:

http://wiki.debian.org/SequenceAlignment

Mafft will be included soon, and T-Coffee will be upgraded shortly after.

Have a nice day,

-- 
Charles Plessy
Debian-Med packaging team
Wako, Saitama, Japan

> 
> ------------------------------------------------------------
> 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)
> life member (LAB, Adventure Cycling, American Youth Hostels)
> Effective Cycling Instructor #218-ck (lapsed)
> Affiliations for identification only.



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