[?] UNIX sequence editor [?]

frist at ccu.umanitoba.ca frist at ccu.umanitoba.ca
Fri Jul 29 10:57:05 EST 1994


In article m9m at osiris.wu-wien.ac.at, seb at i102pc1.vu-wien.ac.at (Sebastian W. Bunka) writes:
> Where can I find a (the sources) sequence editor like "esee"
> for U*IX (Linux; gcc / ansi compiler) ?
> I've tried "mase" from ftp.embl-heidelberg.de but it's for
> SUN and I couldn't compile it (headerfiles missing; different
> library entries...?). Any other programs available?
> 
> Thanks in advance, Sebastian
> 
> --
>                       [ Sebastian.Bunka at vu-wien.ac.at ]
>                         phone:                   FAX:
>                 +43-1-71155260          +43-1-7149110
> Location: earth, europe, austria, vienna  Inst. of Bacteriology  Vet.Univ.


You want GDE, the Genetic Data Environment, by Steven Smith. GDE is a versatile
and easy to use sequence manipulation and analysis program, which includes a
powerful multiple sequence editor.  

The real power of GDE, though, is that it is easy to add new programs to
the menu WITHOUT RECOMPILING! In essense, GDE is a program that
calls other programs. For a given program, a menu is defined in the .GDEmenus file,
and GDE automatically creates an X-windows implementation of that menu. After
program parameters have been set in the menu, GDE runs the program as a 
Unix command.

GDE can be obtained by anonymous FTP to megasun.bch.umontreal.ca in the directory
"pub/gde". Versions are available for LINUX and SUN in this directory.

For an example of how locally installed programs can be called by
GDE see

Fristensky, B. (1993) Feature expressions: creating and manipulating sequence
datasets. Nucl. Acids Res. 21:5997-6003.
(reprints available upon request)

I have added a large number of menu items to GDE, and these are
available by anonymous FTP to ftp.cc.umanitoba.ca in the directory "psgendb".
The file .GDEmenus contains menu items for the following programs, packages,
or email servers:

    XYLEM 
    FSAP 
    FASTA 
    MBCRR 
    PIMA,PLSEARCH 
    ALSCRIPT
    PHYLIP 
    GeneParser 
    DEILIA,DBINST,MAKELOGO 
    PRIMER0.5 

Remember, these are just the menus that call the programs. You still have to
obtain and install each program separately.

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