Finds the best local alignments between two sequences emboss matcher -asequence $input1 -bsequence $input2 -outfile $out_file1 -alternatives $alternatives -gapopen $gapopen -gapextend $gapextend -aformat3 $out_format1 -auto Sequence 1 Sequence 2 Number of alternative matches Gap penalty Gap length (extension) penalty Output Alignment File Format Markx0 (p) Simple (m) FASTA (m) MSF (m) SRS (m) Pair (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/matcher.html