NAME

       cons - Create a consensus sequence from a multiple alignment

SYNOPSIS

       cons -sequence seqset [-datafile matrix] [-plurality float] [-identity integer]
            [-setcase float] -outseq seqout [-name string]

       cons -help

DESCRIPTION

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

OPTIONS

   Input section
       -sequence seqset
           File containing a sequence alignment.

       -datafile matrix
           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.

   Additional section
       -plurality float
           Set a cut-off for the number of positive matches below which there is no consensus.
           The default plurality is taken as half the total weight of all the sequences in the
           alignment. Default value: @( $(sequence.totweight) / 2)

       -identity integer
           Provides the facility of setting the required number of identities at a site for it to
           give a consensus at that position. Therefore, if this is set to the number of
           sequences in the alignment only columns of identities contribute to the consensus.

       -setcase float
           Sets the threshold for the positive matches above which the consensus is is upper-case
           and below which the consensus is in lower-case. Default value: @(
           $(sequence.totweight) / 2)

   Output section
       -outseq seqout

       -name string

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

       cons 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.