aligned sequences editing software

Doug Eernisse DEernisse at fullerton.edu
Sun Feb 7 19:59:30 EST 1999

> In article <tuinen-ya02408000R0302991654290001 at news.inra.fr>,
> tuinen at epoisses.inra.fr (Diederik van Tuinen) wrote:
> >I am looking for a software, hopefully shareware and runing on MacOS,
> >allowing to edit aligned sequences - adding or removing gaps - after a
> >clustalv run.

Besides the other good suggestions already offered, you might find
my "DNA Stacks" software for HyperCard useful. I usually specify
NBRF/PIR or Phylip output file types when using ClustalX or ClustalW
(Phylip will truncate long sequence labels, however), and then
use the "Import Options..." from the Data menu of Aligner stack
(one of the "DNA Stacks") to import the alignment. Some of the
matching/coloring options might also be of interest, for example, 
matching to the first sequence and then coloring according to 
amino acid coding, or amino acid properties, by triplets of DNA.
See also, "Align DNA to Proteins" to place gaps in the corresponding 
DNA file based on the amino acid alignment currently in Aligner.
There are some tutorials from within Aligner that will help with
the somewhat quirky interface of this stack. I like Seq-Al & SeqPup too but
you might find yourself frustrated if much alignment editing is attempted
in any of these. Get DNA Stacks (with Aligner) as freeware
at http://biology.fullerton.edu/deernisse/dnastacks.html
Version 1.0 of the software was released in 1990 and the current '98 
version is 1.2.


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

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