Export sequences

You can access to allele sequences present in the database and specify a list of genes to export with -l option.

Note

The gene list can be obtained with the gene command.

Sequence

A simple export of the different sequences.

wgMLST sequence -h
Usage: wgMLST sequence [OPTIONS] DATABASE

Extracts sequences from a wgMLST DATABASE.

Options:
-o, --output FILENAME  Output result in fasta format (default:stdout).
-f, --file FILENAME    File containing list of coregenes to extract
                       (default:all coregenes).
--reference            Returns reference sequence instead of strain alleles.

MSA

A multialign fasta file with concatenated genes. The file can be used directly for phylogenetic analysis using maximum likelihood or Bayesian approaches.

wgMLST msa -h
Usage: wgMLST msa [OPTIONS] DATABASE

Computes Multiple Sequence Alignment from a wgMLST DATABASE.

Options:
...
-r, --realign          Realigns genes with same length (Default:No).

Warning

It is highly recommended to define a limited list of genes to be exported for the phylogenetic approach.