Plot quality of conservation of a sequence alignment emboss emboss_single_outputfile_wrapper.pl plotcon -sequences $input1 -graph png -goutfile $out_file1 -winsize $winsize -auto Sequence Number of columns to average alignment quality over You can view the original documentation here_. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/plotcon.html