Codon usage analysis

This plugin will analyse the codon usage for individual loci and overall for an isolate. Only loci that have a corresponding database containing sequences, or with sequences tagged, can be included. It is important to note that correct identification of codons can only be achieved for loci for which the correct ORF has been set (if they are not in reading frame 1). Partial sequnces from the sequence bin will not be analysed. Please check the loci that you would like to include. Output is limited to 500 records.

Select ids

Paste in list of ids to include, start a new
line for each. Leave blank to include all ids.

Sequence retrieval

If both allele designations and tagged sequences
exist for a locus, choose how you want these handled:


Select codon order: