This is the command em_conse that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
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 is a command line program from EMBOSS (“the European Molecular Biology Open Software
Suite”). It is part of the "Alignment:Consensus" command group(s).
File containing a sequence alignment.
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.
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)
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.
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)
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