matcher - Waterman-Eggert local alignment of two sequences

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       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).

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

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

       matcher - Waterman-Eggert local alignment of two sequences

Inputsection-asequencesequence-bsequencesequence-datafilematrix
           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.

   Additionalsection-alternativesinteger
           This sets the number of alternative matches output. By default only the highest scoring alignment is
           shown. A value of 2 gives you other reasonable alignments. In some cases, for example multidomain
           proteins of cDNA and genomic DNA comparisons, there may be other interesting and significant
           alignments. Default value: 1

       -gapopeninteger
           The gap penalty is the score taken away when a gap is created. The best value depends on the choice
           of comparison matrix. The default value of 14 assumes you are using the EBLOSUM62 matrix for protein
           sequences, or a value of 16 and the EDNAFULL matrix for nucleotide sequences. Default value:
           @($(acdprotein)? 14 : 16)

       -gapextendinteger
           The gap length, or gap extension, penalty is added to the standard gap penalty for each base or
           residue in the gap. This is how long gaps are penalized. Usually you will expect a few long gaps
           rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. An
           exception is where one or both sequences are single reads with possible sequencing errors in which
           case you would expect many single base gaps. You can get this result by setting the gap penalty to
           zero (or very low) and using the gap extension penalty to control gap scoring. Default value:
           @($(acdprotein)? 4 : 4)

   Outputsection-outfilealign

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

matcher-asequencesequence-bsequencesequence [-datafilematrix] [-alternativesinteger]
               [-gapopeninteger] [-gapextendinteger] -outfilealignmatcher-help