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cons - Create a consensus sequence from a multiple alignment


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

cons -help


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).


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

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