NAME

       allversusall - Sequence similarity data from all-versus-all comparison.

SYNOPSIS

       allversusall -seqinpath dirlist [-matrix matrixf] [-gapopen float] [-gapextend float]
                    -datoutdir outdir -logfile outfile

       allversusall -help

DESCRIPTION

       allversusall is a command line program from EMBOSS (“the European Molecular Biology Open
       Software Suite”). It is part of the "Utils:Database creation" command group(s).

OPTIONS

   Input section
       -seqinpath dirlist
           Default value: ./

       -matrix matrixf
           This option specifies the residue substitution matrix that is used for sequence
           comparison. Default value: EBLOSUM62

   Required section
   Additional section
       -gapopen float
           This option specifies the gap insertion penalty. The gap insertion penalty is the
           score taken away when a gap is created. The best value depends on the choice of
           comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for
           protein sequences, and the EDNAFULL matrix for nucleotide sequences. Default value: 10

       -gapextend float
           This option specifies the gap extension penalty. The 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
           open penalty to zero (or very low) and using the gap extension penalty to control gap
           scoring. Default value: 0.5

   Output section
       -datoutdir outdir
           This option specifies the location of sequence similarity data files (output). Default
           value: ./

       -logfile outfile
           This option specifies the name of ALLVERSUSALL log file (output). The log file
           contains messages about any errors arising while ALLVERSUSALL ran. Default value:
           allversusall.log

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

       allversusall 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.