This program will read in data from an ABI 3700, 3100, 377 or 373, CEQ 2000 or SCF and reconstruct them into a gel image which is straightened and sized. Bins can be defined easily and viewed as thumbnails, which allows for a fairly quick and easy way of scoring a gel.
The program is written in Java and uses the Java 1.3 API. Therefore, it should run on any machine that can run java. See Installing and Running for more info.
For a more thourough description of the programs capabilities, see the help files. The tutorial provides a fairly good overview of the program.
This program is distributed under the GNU General Public Liscense.
Current version is 1.6
Released October 14, 2001
There are several options for downloading. One can download the complete program (includes source code and demo data), the program with just demo data, the program with source code, or only the program files required to run the program. The source code can be downloaded seperately later (see below). Only one of these files is needed. The files are given both as zip files for PCs and tar.gz files for UNIX/Linux. The contents of the files is identical.
Please: I would appreciate an email if you decide to download the program (james_benham@hmc.edu) so that I can get an idea of how many people are using the program and inform them of updates. (If you don't want to here about updates, just say so.)
Previous versions of Genographer are available in the archive.
The help files are also available on the WWW at:
http://hordeum.oscs.montana.edu/genographer/help/help.html
To upgrade, simply extract to the same location and overwrite the files. The only complication will be if you editted standards.cfg or genograph.cfg. Simply keep your old standards.cfg. Version 1.1 added a parameter to genograph.cfg which should be added. Simply back up your old config file, open both the new and the old in a text editor, and merge them together. It should be really easy. If you didn't modify either of these files, don't worry about it.
Genographer 1.4 added a size standard, which seems to be in fairly common use. When upgrading, make sure that the new standard is in the standards.cfg file you are using.
These files contain the source code and the source code documentation. If they are extracted into the same directory as the program, they will be inserted into the correct spot.
The directory structure for the source file is as follows
+--genographer
+--src
+--AFLPcore (program data structures and algorithms)
+--AFLPgui (program gui interface)
+--doc
+--src (source code documentation)
+--images (images for the documentation)
This should line up nicely with the programs directory structure.
Contact VisualTek for the source to the Java PNG library.
Send questions to
james_benham@hmc.edu or
Tom Blake < blake@hordeum.msu.montana.edu>
Phil de Camp did the v1.5 and SCF, so you may want to try him for SCF
related questions.
decamp@portalofevil.com