Amino Acid Alignment Formating

[James O. McInerney]

Jeffrey J. Huckaby wrote:

> Netters
>         I am search for a Mac and/or Unix SunOS program that formats
> multiple sequence alignments for publication such that the similar 
> amino acids are shaded and the identities are boxed...or some format 
> close to this one.

Have you tried seqapp/seqpup (all platforms incl MacOS) by Don Gilbert 
at 


  <ftp://iubio.bio.indiana.edu/molbio/seqpup/>
  <gopher://iubio.bio.indiana.edu/11/IUBio-Software+Data/molbio/seqpup/>
  <http://iubio.bio.indiana.edu/1/IUBio-Software%2bData/molbio/seqpup/>

This should do what you want.  Lots of bells and whistles.  Careful, 
though and save often and it still is not bug-free.

james