cons -sequence seqset [-datafile matrix] [-plurality float] [-identity integer] [-setcase float] -outseq seqout [-name string]
- cons -help
- 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)
Debian Med Packaging Team <[email protected]>
- Wrote the script used to autogenerate this manual page.
This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself.