Laj 070222 – Alignment Viewer

Laj 070222


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.



Cathy Riemer



  • Windows/ Linux / Mac OsX
  • JAVA





Wilson MD, Riemer C, Martindale DW, Schnupf P, Boright AP, Cheung TL, Hardy DM, Schwartz S, Scherer SW, Tsui LC, Miller W, Koop BF.
Comparative analysis of the gene-dense ACHE/TFR2 region on human chromosome 7q22 with the orthologous region on mouse chromosome 5.
Nucleic Acids Res. 2001 Mar 15;29(6):1352-65.

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