| Species | Codon table file name |
| green algae | algae.cod |
| Aspergillus nidulans | asn.cod |
| Arabidopsis thaliana | ath.cod |
| Hordeum vulgare (Barley) | bly.cod |
| Bombyx mori (Silk Moth) | bmo.cod |
| Bos taurus (Cow) | bov.cod |
| Bacillus subtilis | bsu.cod |
| Caenorhabditis elegans | cel.cod |
| Chironomus sp. | chi.cod |
| Gallus sp. (Chicken) | chk.cod |
| Chlamydomonas | cre.cod |
| Dictyostelium discoideum | ddi.cod |
| Drosophila melanogaster | dro.cod |
| Escherichia coli | eco.cod |
| enteric bacterial (highly expressed) genes | ecohigh.cod |
| Cricetulus sp. & Mesocricetus sp. (Hamster) | ham.cod |
| Homo sapiens | hum.cod |
| Klebsiella pneumoniae | kpn.cod |
| Macaca sp | mac.cod |
| Mus sp. (Mouse) | mus.cod |
| Zea mays (Maize) | mze.cod |
| Zea mays chloroplast (Maize) | mzecp.cod |
| Neurospora crassa | neu.cod |
| Neisseria gonorrheae | ngo.cod |
| Pisum sativum (Pea) | pea.cod |
| Petunia sp. | pet.cod |
| Plasmodium falciparum | pfa.cod |
| Phaseolus vulgaris (Lima bean) | phv.cod |
| Solanum tuberosum (Potato) | pot.cod |
| Pseudomonas sp. | pse.cod |
| Oryctolagus sp. (Rabbit) | rab.cod |
| Rattus sp. (Rat) | rat.cod |
| Rhizobium meliloti | rhm.cod |
| Oryza sativa (Rice) | ric.cod |
| Ovis sp. (Sheep) | shp.cod |
| Physarum polycephalum | slm.cod |
| Glycine max (Soybean) | soy.cod |
| Staphylococcus aureus | sta.cod |
| Salmonella thphimurium | sty.cod |
| Strongylocentrotus purpuratus | sus.cod |
| Tetrahymena thermophila | tet.cod |
| Nicotiana tabacum (Tobacco) | tob.cod |
| Nicotiana tabacum chloroplast (Tobacco) | tobcp.cod |
| Lycopersicon esculentum (Tomato) | tom.cod |
| Trypanosoma brucei | trb.cod |
| Triticum aestivum (Wheat) | wht.cod |
| Xenopus laevis | xel.cod |
| Saccharomyces cerevisiae | ysc.cod |
| Saccharomyces cerevisiae mitochondrion | yscmt.cod |
| Schizosaccharomyces pombe | ysp.cod |
For details about any of these tables, extract the actual table by typing 'fetch xxx.cod' at the helix prompt, and read the documentation at the top of the file.
To use any of these codon tables instead of the default (E.Coli) table, add the parameter '-translate=xxx.cod' when running any of the above programs.
If you need a codon table that is not in this list, send mail to the helix staff using the ptr command on helix (type 'ptr' at the helix prompt) and we will attempt to track it down for you.