Match large sequences against one or more other sequences emboss supermatcher -asequence $input1 -bsequence $input2 -gapopen "$gapopen" -gapextend "$gapextend" -width "$width" -wordlen "$wordlen" -outfile $ofile1 -errorfile $ofile2 -aformat3 $out_format1 -auto Large sequences Sequences to match Gap opening penalty Gap extension penalty Alignment width Word length for initial matching Output Alignment File Format Simple (m) FASTA (m) MSF (m) SRS (m) Pair (p) Markx0 (p) Markx1 (p) Markx2 (p) Markx3 (p) Markx10 (p) SRS pair (p) Score (p) You can view the original documentation here_. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/supermatcher.html