Multiple sequence alignment software???

Dr. Peter Gegenheimer PGegen at
Fri Feb 20 20:36:40 EST 1998

On Thu, 19 Feb 1998 15:23:26, Tburglin
<burglin at> wrote:

> Does anybody know of a good multiple sequence alignment software
> for protein and DNA that works either under Unix or on the Macintosh?

The only program I know of which lets you drag sequences around and
"nudge" individual residues into alignment is GeneDoc, from the
Pittsburgh Supercomputer Center. This is professionally-0coded and
scientifically state-of-the-art software which is mind-boggling if
you have never used it before. It runs under Windows (not sure of
other platforms), but has _no_ competition. Residues can be
highlighted according to conservation, chemical properties, 3D
structure, etc. It imports several multiple alignment files, but its
native format is MSF (GCG format, isn't it). Also imports results of
protein secondary structure prediction or xtal structures and
displays the features by highlighting. It is currently free.

The GeneDoc homepage is

| Dr. Peter Gegenheimer       |  Vox: 785-864-3939  FAX:
785-864-5321 |
| Departments of Biochemistry |    PGegen at
|  and of Botany              |
|                             |
| University of Kansas        |
| 2045 Haworth Hall           |  "The sleep of reason produces
| Lawrence  KS  66045-2106    |   monsters."                  Goya

More information about the Bio-soft mailing list