cons - Create a consensus sequence from a multiple alignment

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

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).

       cons - Create a consensus sequence from a multiple alignment

Inputsection-sequenceseqset
           File containing a sequence alignment.

       -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-pluralityfloat
           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)

       -identityinteger
           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.

       -setcasefloat
           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)

   Outputsection-outseqseqout-namestring

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

cons-sequenceseqset [-datafilematrix] [-pluralityfloat] [-identityinteger] [-setcasefloat]
            -outseqseqout [-namestring]

       cons-help