Question about multiple sequence alignment

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

In article <7n8360$2n4$1 at>, David Jones
<jones at> 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.



Doug Eernisse
Department of Biological Science
California State University
Fullerton, CA 92834-6850 USA

More information about the Bio-soft mailing list