aligning NA sequences based upon translation

Ashok Aiyar aiyar at ebv.oncology.wisc.edu
Tue Mar 17 17:59:47 EST 1998

On 17 Mar 1998 12:56:14 -0500,
Allan Strand (astrand at linum.cofc.edu) wrote:

>I'm looking for software that will align multiple nucleic acid
>sequences based upon their translations into amino acid sequences.
>That is, I would like the input and output of the algorithm to be
>nucleic acid coding sequences, but I want the actual alignment to be
>determined by the amino acid sequence implied by these NA sequences.

You should take a look at Burkhard Morgenstern's program DIALIGN.
It does exactly what you would like it to.  Binaries are available
for a number of Unix platforms from:

In addition, because the GNU C compiler has been ported to Win95/WinNT,
it would not be difficult to make binaries available for those operating 
systems as well.

Ashok Aiyar, Ph.D.
McArdle Laboratory for Cancer Research
aiyar at ebv.oncology.wisc.edu

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