? about DNA alignment

[Jeremy John Ahouse]

Here is the problem,

    I have done a series of multiple alignments.  The alignments were done
with inferred amino acid sequences.  Now that I am happy with the
alignments I want to go back to the mRNA sequence (which I have) for some
of the clustering and parsimony analysis.  I want to enforce the alignments
(gaps, etc...) from the aa's on the nucleotide alignment.

    I know I can do this by hand, but are there any tools that help with
this, that you all know about?

    - Jeremy

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        Jeremy John Ahouse
        Center for Complex Systems and Biology Dept
        Brandeis University
        Waltham, MA 02254-9110
        (617) 736-4954
        email: ahouse at hydra.rose.brandeis.edu
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