Please recommend a DNAanalysis software package?

Ashok Aiyar aiyar at ebv.oncology.wisc.edu
Wed Jan 13 10:49:06 EST 1999

On 13 Jan 1999 09:58:36 GMT,
    Stephane Bortzmeyer (bortzmeyer at pasteur.fr) wrote:
>In article <3695BBA3.6334E2E1 at utu.fi>,
> Amir Snapir <snapir at utu.fi> writes:
>> Have a look at Prophet ( http://www.utu.fi/med/farmakol/prophet/ ). It's not bug
>> free and it has little tendency to crash (somehow even when it crashes you don't
>> loose your work) but fairly powerful and... it's free!
>"Free" as in "free beer" (you pay nothing) but not as in "free speech".
>I don't find the sources? Apparently, it runs only on MS-Windows?

Hello Stephane,

    You are correct; Prophet is free as in "free beer".  My recollection
is that the home site "www-prophet.bbn.com" had versions for some unices
available -- notably Solaris/SPARC, but not Linux on any platform.  One
of their programmers / website caretaker had stated on this newsgroup that:

a) a Linux version was not available because the widget-set they used on
   Solaris and Windows were not available for Linux (it wasn't Motif, or
   Qt -- I cannot remember the name).
b) that sources were not available because they were too large to download

    I responded to him on point "b", offering to send him a blank tape, or 
the archival space and bandwidth that others might download it, and was then
informed that their contract with NIH prevented them from distributing the

    That's unfortunate because most programs developed at NCBI itself 
appear to be distributed as source (the NCBI toolkit is a prominent example),
which facilitates porting applications to many many more platforms than
can be done by a single group of programmers.  Not to mention the 
intellectual advantages of open-source software.

    Sorry for the proselytizing -- I firmly believe, as I am sure you do,
that scientific software would greatly benefit from being open-source.

Ashok Aiyar, Ph.D.
McArdle Laboratory for Cancer Research

More information about the Bio-soft mailing list

Send comments to us at biosci-help [At] net.bio.net