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LEARN ABOUT DEBIAN

allversusall

ALLVERSUSALL(1e)					     EMBOSS Manual for Debian						  ALLVERSUSALL(1e)

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.

DOMALIGN 0.1.0+20100721 					    08/11/2010							  ALLVERSUSALL(1e)