www.genographer.com      GenographerDAxContact Information
DAx and Genographer
           

Gel Scoring Software


 
Genographer is a software package for gel scoring. Its home page is located at http://hordeum.oscs.montana.edu/genographer/. Genographer is distributed under the GNU General Public License. Genographer is distributed free of charge.

DAx is a commercial software package for analysis of chemical data, including gel scoring of genotyping data. Its home page is located at http://www.dax.nl. While DAx is not free of charge, it offers a number of advantages over Genographer.
  • DAx is updated regularly to cope with users' changing needs (the Genographer home page indicates it has not been updated since 2001);
  • ability to read all ABI Genescan® files (*.fsa, *.abi), including ABI 3730 files;
  • ability to read Amersham MegaBACE™ files (*.rsd, *.esd);
  • ability to read and handle ABI files that have not been called yet with Genescan®, as well as ABI files for which no BP calibration has been determined yet.
    BP sizes of standard peaks can be read from ABI files, with no need to have a separate standards.cfg file;
  • fully featured baseline construction / peak find ability;
  • simultaneous display of colour view (gel view) and binning sheet containing curve samples;
  • easy maintenance of user defined bins (including easy deletion);
  • fully customisable colours and sizes;
  • binning sheet export of PHYLIP and PAUP formats; binning sheet export of tab delimited text files (including full column labels); binning sheet export of thumbnail views as RTF Word Processor files;
  • ability to handle several thousand files simultaneously;
  • DAx is fully compatible with Windows™ 9x, Me, 2000, XP;
  • fully supported software: problems are solved generally within 24 hours.

DAx will readily load data from ABI Genescan® fragment analysis files (*.fsa, *.abi), Amersham MegaBACE™ files (*.rsd, *.esd), as well as Staden SCF files (*.scf). Sizing information is retrieved from the file, or can be readily derived using Automatic Trace Calibration (ATC).
The data are displayed either as traces or as a colour view "gel" image, with either a calibrated or unaltered axis.

Calibrated colour view of 11 data files, with 3 traces in each file displayed (ROX - red, FAM - green, and HEX - blue)
Calibrated colour view of 11 data files, with 3 traces in each file displayed per lane (ROX - red, FAM - green, and HEX - blue).
Traces can also be displayed individually, one per lane.


DAx uses powerful binning sheets to display data on peaks in multiple traces.
Bins can be defined by entering lower and upper limits manually, or by double clicking on, or clicking & dragging the mouse across a band in the colour view.
Each bin in the binning sheet can be displayed on a single line or wrapped across multiple lines. Trace samples ("thumbnails") can be displayed in the binning sheet. The user can mark or unmark peaks by double clicking on the trace samples.

Colour view with user defined bins, and binning sheet showing only the fifth bin with trace samples
Colour view with user defined bins, and binning sheet showing only the fifth bin with trace samples.
Note the faint yellow tooltip window displaying specifics about the peak under the mouse cursor.
When the mouse is moved over the colour view, the appropriate cell in the binning sheet is brought into view and highlighted.



For a detailed manual on how to use DAx to score gels, click here.