Non-overlapping wordmatch dotplot of two sequences emboss emboss_single_outputfile_wrapper.pl dotpath -asequence $input1 -bsequence $input2 -goutfile $out_file1 -wordsize $wordsize -overlaps $overlaps -boxit $boxit -graph png -auto Sequence 1 Sequence 2 Word size (Integer 2 or more) Display the overlapping matches (in red) as well as the minimal set of non-overlapping matches No Yes Draw a box around dotplot Yes No You can view the original documentation here_. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dotpath.html