wordfinder - Match large sequences against one or more other sequences

DebianMedPackagingTeam <debian-med-packaging@lists.alioth.debian.org>
           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
       redistributed under the same terms as EMBOSS itself.

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

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

       wordfinder - Match large sequences against one or more other sequences

Inputsection-asequenceseqset-bsequenceseqall-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.

   Requiredsection-gapopenfloat
           Default value: @($(acdprotein)? 30.0 : 30.0)

       -gapextendfloat
           Default value: @($(acdprotein)? 1.5 : 1.5)

   Additionalsection-widthinteger
           Default value: 16

       -wordleninteger
           Default value: 6

       -limitmatchinteger-limitaligninteger-lowmatchinteger-lowalignintegerOutputsection-outfilealign-errorfileoutfile
           Error file to be written to Default value: wordfinder.error

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

wordfinder-asequenceseqset-bsequenceseqall [-datafilematrixf] -gapopenfloat-gapextendfloat
                  [-widthinteger] [-wordleninteger] [-limitmatchinteger] [-limitaligninteger]
                  [-lowmatchinteger] [-lowaligninteger] -outfilealign [-errorfileoutfile]

       wordfinder-help