Information About Laj

Laj is a tool for viewing and manipulating the output from pairwise alignment programs such as blastz. It can display interactive dotplot, pip, and text representations of the alignments, a diagram showing the locations of exons and repeats, and annotation links to other web sites containing additional information about particular regions.

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 "Local Alignments with Java". Currently it exists in two forms, a stand-alone application and a web-based applet, with slightly different capabilities.

Applet demo:  using Sun's Java Plug-in | using your browser's default Java

The current Laj distribution package is available for download as a compressed zip archive,  laj.zip .

The following documentation files are included:

• What's New
  A summary of the changes in each released version of Laj.

• Laj as a Stand-Alone Application
  Describes how to install and run Laj as a stand-alone application on your own computer.

• Installing Laj as an Applet
  Describes how to install Laj as an applet on your web server, so other people can view your data.

• Installing the Java Plug-in
  Information to help web browsers work correctly with the Laj applet.

• Help Page for the Laj Applet
  The applet's help button displays this help page for applet users.

• Input File Formats for Laj
  Detailed descriptions of the input file formats for both forms of Laj.

• Implementation Notes
  For those who may be interested, a little general information about how Laj is organized inside.