NAME

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

SYNOPSIS

       supermatcher -asequence seqall -bsequence seqset [-datafile matrixf] [-minscore float] -gapopen float
                    -gapextend float [-width integer] [-wordlen integer] -outfile align [-errorfile outfile]

       supermatcher -help

DESCRIPTION

       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).

OPTIONS

   Input section
       -asequence seqall

       -bsequence seqset

       -datafile matrixf
           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.

       -minscore float
           Minimum alignment score to report an alignment.

   Required section
       -gapopen float
           Default value: @($(acdprotein)? 10.0 : 10.0)

       -gapextend float
           Default value: @($(acdprotein)? 0.5 : 0.5)

   Additional section
       -width integer
           Default value: 16

       -wordlen integer
           Default value: 6

   Output section
       -outfile align

       -errorfile outfile
           Error file to be written to for failed alignments Default value: supermatcher.error

BUGS

       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).

SEE ALSO

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

AUTHOR

       Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
           Wrote the script used to autogenerate this manual page.

COPYRIGHT

       This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be
       redistributed under the same terms as EMBOSS itself.

EMBOSS 6.4.0                                       05/11/2012                                   SUPERMATCHER(1e)