Question about multiple sequence alignment

Doug Eernisse DEernisse at fullerton.edu
Sun Jul 25 20:12:39 EST 1999


In article <7n8360$2n4$1 at holly.csv.warwick.ac.uk>, David Jones
<jones at globin.bio.warwick.ac.uk> wrote:

> The bottom line is that both methods are going to produce alignments which
> are not biologically correct - so why not use the faster approximate method?
> 
> On a more practical note, we are now facing situations where we now have
> to produce good multiple alignments for hundreds or even thousands of
> sequences. Even the faster approximate MSA programs take a long time to
> align this many sequences.
> 

Just out of curiosity, does anyone have empirical experience with
how many sequences can be aligned with the current version of Clustal (1.8)?
I was surprised that I could do something like 69 sequences without
much problem on my Mac G3 (Clustal X, rDNA sequences about 1.8 kb average,
default settings). Now I am wondering how many I could do if I waited longer 
or installed Clustal W on a Unix box. I am suspecting that Clustal is
about as fast as any, reasonably effective, program, but please 
enlighten me if I am wrong.

Thanks.



Doug

-- 
Doug Eernisse
Department of Biological Science
California State University
Fullerton, CA 92834-6850 USA
<http://biology.fullerton.edu/deernisse/>





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