Displays a wordmatch dotplot of two sequences emboss emboss_single_outputfile_wrapper.pl dottup -asequence $input1 -bsequence $input2 -goutfile $out_file1 -wordsize $wordsize -boxit $boxit -graph png -xygraph png -auto Sequence 1 Sequence 2 Word size 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/dottup.html