https://github.com/hyattpd/prodigal/wiki/cheat-sheet
Prodigal supports all genetic codes defined by NCBI. Most bacteria and archaea use genetic code 11, which uses three stop codons (TAA, TGA, and TAG). Some bacteria do not use TGA as a stop codon. Mycoplasma, spiroplasma, and ureaplasma translate UGA to tryptophan (W) (genetic code 4), while bacteria using genetic code 25 translate UGA to glycine (G).
By default, Prodigal tries genetic code 11. If the average gene length is too low, it tries genetic code 4. If the average gene length is still too low, it reverts back to genetic code 11 and outputs a warning.
https://github.com/hyattpd/prodigal/wiki/cheat-sheet
Prodigal supports all genetic codes defined by NCBI. Most bacteria and archaea use genetic code 11, which uses three stop codons (TAA, TGA, and TAG). Some bacteria do not use TGA as a stop codon. Mycoplasma, spiroplasma, and ureaplasma translate UGA to tryptophan (W) (genetic code 4), while bacteria using genetic code 25 translate UGA to glycine (G).
By default, Prodigal tries genetic code 11. If the average gene length is too low, it tries genetic code 4. If the average gene length is still too low, it reverts back to genetic code 11 and outputs a warning.