Gmaj: an Interactive Viewer for Multiple Sequence Alignments

Gmaj is a tool designed for viewing and manipulating Generalized Multiple Alignments (GMAs) produced by sequence-symmetric alignment programs such as TBA (though it can also be used with MAF format alignments from other sources). It can display interactive graphical and text representations of the alignments, diagrams showing the locations of exons and repeats, and other annotations -- all with the user's choice of reference sequence.

The program is written in Java in order to provide a graphical user interface that is portable across a variety of computer platforms; indeed its name stands for "Generalized Multiple Alignments with Java". It requires Java 1.3 or higher, and for best compatibility Sun's JRE (or JDK) is recommended.

Gmaj can be run in two different modes: as a stand-alone application (for viewing local data files yourself) or as an applet over the world-wide web (to display your data on a server for viewing by others). These modes are mostly similar, but have a few minor differences due to the underlying capabilities of applets vs. applications in Java.

Applet demo

The current Gmaj distribution package is available for download as a compressed zip archive, gmaj.zip.

The following additional documentation files are included:

• What's New in Gmaj
  A summary of the changes in each released version of Gmaj. (Note important bug fix on 2005-Sep-13.)

• Known Bugs in Gmaj
  A discussion of the known bugs and anomalies we have observed, but not yet resolved. Some of these may depend on your computer platform and/or version of Java.

• Installing Gmaj
  Describes how to unpack and set up Gmaj, for both stand-alone and applet use.

• Starting and Running Gmaj
  Describes how to start Gmaj and use the GUI, in both stand-alone and applet modes. This is the file that Gmaj's "Help - Manual" menu item points to.

• Input Files for Gmaj
  Detailed descriptions of the input files used by Gmaj, and their formats.

• sample.gmaj
  A sample template for the parameters file that tells Gmaj which data files to load, among other things. Includes explanatory comments at the bottom. This file is optional if you don't want to display any annotations or use the other features it provides.