Pairwise Alignment Viewer LAJ.py $maf_input $out_file1 You can use this tool to view a set of LAV alignments. You may include FASTA formatted sequences for both species. For detailed information on LAJ, click here_. .. _here: http://globin.cse.psu.edu/dist/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. .. class:: infomark **Note:** If you save output from the applet, you will need to manually refresh your history. @misc{Miller2005, author = {Miller Lab}, year = {2005}, title = {Laj}, url = {http://globin.bx.psu.edu/dist/laj/}, }