Smith-Waterman local alignment emboss water -asequence $input1 -bsequence $input2 -outfile $out_file1 -gapopen "$gapopen" -gapextend "$gapextend" -brief $brief -aformat3 $out_format1 -auto Sequence 1 Sequence 2 Gap open penalty Gap extension penalty Brief identity and similarity Yes No Output Alignment File Format SRS (m) Simple (m) FASTA (m) MSF (m) Pair (p) Markx0 (p) Markx1 (p) Markx2 (p) Markx3 (p) Markx10 (p) SRS pair (p) Score (p)

.. class:: warningmark The input datasets need to be sequences. ----- You can view the original documentation here_. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/water.html