em_cons1e
Create a consensus sequence from a multiple alignment
Part of cons(1e).
Usage
cons -sequence
seqset
[-datafile
matrix]
[-plurality
float]
[-identity
integer]
[-setcase
float]
-outseq
seqout
[-name
string]
cons -help
Overview
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
History
- Debian 13 (Trixie) to Debian 7 (Wheezy): the text shown here
- Debian 6.0 (Squeeze)