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.