Can DNAsis replace GCG package? Or almost??

Brian Fristensky frist at ccu.umanitoba.ca
Thu Oct 6 16:17:44 EST 1994

In article gtq at mace.cc.purdue.edu, xniu at mace.cc.purdue.edu (Xiaomu Niu) writes:
> 	We narrowed our choices down to two:
> 		(1) a 486/586 pc running linux and X-windows
> 		(2) a Machintosh or a Power Mac
> 	With the first one, we can run MS-Windows with Hitachi's
> DNAsis for window, or we install Linux and run GDE plus other freely
> availabe sequence analysis programs for unix, something like BIRCH 
> (but running on a pc).
> 	With the second choice, we probably have to purchase the    
> MacDNAsis from Hitachi. Or we can try GeneWorks (?) also.
> 	But here is the question: (sorry for the long introduction)
> Can DNAsis replace GCG completely or nearly? What about speed? It
> seems we have people here running DNAsis on a Mac SE with a CD-ROM
> happily. If we understand right, GDE covers most of GCG's functions,
> and it's available for free.
One of the main reasons for creating BIRCH in the first place (aside from the
fact that I had free access to Unix workstations and NO FUNDS to buy
commercial software) was that there is no such thing as a package that
does everything. GCG does some things better than most other packages, some
things less well, and many things not at all. The same will be true of 
DNAsis, GeneWorks, the Staden programs, or any single package. No one 
package does everything, and certainly none do everything well.

BIRCH is nothing more than a hierarchical directory structure of databases, 
programs, and documentation. The beauty of GDE is that it is trivial to add
new programs to the 
menus. If you tie yourself to a single commercial package, you have only
the capabilities that the authors build into it, and have to interconvert
file formats when you want to use programs from elsewhere. On a system
such as BIRCH, we can mix and match programs from many sources, letting
GDE take care of converting file formats for us. At the same time, all of
the programs from the various packages (eg. FASTA, XYLEM, FSAP, PHYLIP, MBCRR,
Oxford, etc.) are still useable as standalone programs, if desired.

Brian Fristensky                | 
Department of Plant Science     |  A question is like a knife that slices
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frist at cc.umanitoba.ca           |  
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