supermatcher - Calculate approximate local pair-wise alignments of larger sequences

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           Wrote the script used to autogenerate this manual page.

       Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to
       the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031).

       This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be
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EMBOSS 6.4.0                                       05/11/2012                                   SUPERMATCHER(1e)

supermatcher is a command line program from EMBOSS (“the European Molecular Biology Open Software
       Suite”). It is part of the "Alignment:Local" command group(s).

       supermatcher - Calculate approximate local pair-wise alignments of larger sequences

Inputsection-asequenceseqall-bsequenceseqset-datafilematrixf
           This is the scoring matrix file used when comparing sequences. By default it is the file 'EBLOSUM62'
           (for proteins) or the file 'EDNAFULL' (for nucleic sequences). These files are found in the 'data'
           directory of the EMBOSS installation.

       -minscorefloat
           Minimum alignment score to report an alignment.

   Requiredsection-gapopenfloat
           Default value: @($(acdprotein)? 10.0 : 10.0)

       -gapextendfloat
           Default value: @($(acdprotein)? 0.5 : 0.5)

   Additionalsection-widthinteger
           Default value: 16

       -wordleninteger
           Default value: 6

   Outputsection-outfilealign-errorfileoutfile
           Error file to be written to for failed alignments Default value: supermatcher.error

       supermatcher is fully documented via the tfm(1) system.

supermatcher-asequenceseqall-bsequenceseqset [-datafilematrixf] [-minscorefloat] -gapopenfloat-gapextendfloat [-widthinteger] [-wordleninteger] -outfilealign [-errorfileoutfile]

       supermatcher-help