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.
The current Gmaj distribution package is available for download
as a compressed zip archive,
The following additional documentation files are included: