stand-alone equivalent of PRETTY

John Watson watson_j at bms.com
Fri Nov 1 12:32:41 EST 1996

ijohn at london.biology.lsa.umich.EDU (Isaac John) wrote:

>I think "DNA Star" does better than pretty. It is PC based and very simple
>to use.
>On 31 Oct 1996, Les Klimczak wrote:
>>       We are trying to become less dependent on the GCG package,
>> especially since many PC- and Web-based programs provide parts of its
>> functionality and the fees/costs of maintaining GCG have not declined in
>> a noticable way. Our only "missing link" in making graphically enhanced
>> sequence alignments in the function of PRETTY - identification of similar
>> amino acids, as defined by a similarity matrix such as PAM250, and
>> labeling of the identified ones with uppercase.
>>       Does anyone know of any stand-alone program/macro/script that
>> would perform this function? TIA.

We use the DNAStar application MegAlign to perform Macintosh desktop
PILEUP/PRETTY/PRETTYPLOT functions, but it is not cheap.  As I recall, it
was not available in site-license form, and wehad to purchase a number of
individual licenses.  To be fair, the cost does drop the more copies you

On the freeware side, I have heard repeated claims that Macaw from NCBI and
SeqPup, Don Gilbert's program, give the same functionality as
PILEUP/PRETTY, but I cannot vouch for either.



    __ __ __       A. John Watson, Ph.D.
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