cons calculates a consensus sequence from a multiple sequence alignment.

Here is a sample session with cons:

% cons
Creates a consensus from multiple alignments
Input sequence set: aligned.fasta
Output file [outfile.cons]: aligned.cons

Mandatory qualifiers:

[-msf] (seqset)

File containing a sequence alignment.

[-outseq] (seqout)

Output sequence USA.

Optional qualifiers:

-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.

-plurality (float)

Set a cutoff 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.

-identity (integer)

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

-name (string)

Name of the consensus sequence.

-setcase (float)

Sets the threshold for the positive matches. Residues in the consensus sequence have their case determined by this threshold: those above it are in uppercase; those below it are in lowercase.