CODEHOP Codon Usage Tables

Bacteria (gbbct):
Acholeplasma laidlawii
Agrobacterium tumefaciens
Bacillus subtilis
Bacillus thuringiensis
Bartonella bacilliformis
Bartonella henselae
Brucella abortus
Campylobacter jejuni
Chlamydia trachomatis
Chlorobium limicola Green sulfur bacteria
Chlorobium vibrioforme Green sulfur bacteria
Chlorobium tepidum Green sulfur bacteria
Clostridium botulinum
Crenarchaeota (User-contributed)
Ehrlichia chaffeensis
Escherichia coli
Euryarchaeota (User-contributed)
Haemophilus influenzae
Halobacterium sp. NRC-1
Helicobacter pylori 26695
Lactobacillus casei
Leptospira interrogans
Myxococcus xanthus
Pantoea agglomerans
Paracoccus denitrificans
Pseudomonas syringae pv. glycinea
Ralstonia eutrophia
Rhizobium leguminosarum
Rhodobacter sphaeroides
Rhodococcus erythropolis
Sinorhizobium meliloti
Staphylococcus aureus
Streptomyces coelicolor
Sulfolobus solfataricus
Synechococcus sp.
Xanthomonas oryzae pv. oryzae
Unknown flavobacteria (User-contributed)

Invertebrates (gbinv):
Acanthamoeba castellanii
Acropora millepora Hard coral
Ancylostoma canium Dog hookworm
Ascaris suum Pig roundworm
Bivalve mollusks (User-contributed)
Blattella germanica German cockroach
Bombyx mori Silkworm
Brugia malayi
Caenorhabditis elegans Nematode
Callinectes sapidus Blue crab
Cephalopods (User-contributed)
Culex pipiens House mosquito
Dictyostelium discoideum Soil amoeba
Drosophila melanogaster Fruit fly
Entamoeba histolytica
Geodia cydonium
Giardia intestinalis
Haemonchus contortus
Helicoverpa armigera
Heliothis virescens
Heterodera glycines Soybean cyst nematode
Hirudo medicinalis
Hydra vulgaris
Lasius niger Black ant (User-contributed)
Leishmania major
Leishmania tarentolae
Litopenaeus vannamei Pacific white shrimp
Lucilia cuprina Dipteran
Lymnaea stagnalis Pond snail
Musca domestica House fly
Mytilus edulis Blue mussel
Mytilus galloprovincialis Mediterranean mussel
Myzus persicae Green peach aphid
Onchocerca volvulus
Placopecten magellanicus Sea scallop
Plasmodium falciparum
Podocoryne carnea Jellyfish
Schistosoma mansoni
Strongylocentrotus purpuratus
Suberites domuncula
Tetrahymena pyriformis
Tetrahymena thermophila
Trichinella spiralis
Trichomonas vaginalis
Trypanosoma brucei

Mammals (gbmam):
Bos taurus Cow
Canis familiaris Dog
Equus caballus Horse
Oryctolagus cuniculus Rabbit
Ovis aries Sheep
Sus scrofa Pig

Plants and Fungi (gbpln):
Alnus glutinosa European alder
Antirrhinum majus Snapdragon
Arabidopsis thaliana Thale cress
Aspergillus fumigatus
Aspergillus nidulans
Brassica napus Rape
Brassica oleracea Broccoli, etc.
Camptotheca acuminata
Ceratopteris richardii Fern
Chara corallina Charophyte
Chlamydomonas reinhardtii
Citrus sinensis Navel orange
Clarkia breweri
Clarkia concinna
Dunaliella salina
Emericella nidulans
Eschscholzia californica California poppy
Euglena gracilis
Fabaceae family (User-contributed)
Ginkgo biloba
Glycine max Soybean
Gonyaulax polyedra Alga
Gossypium hirsutum Cotton
Hordeum vulgare Barley
Lotus corniculatus var. japonicus Lotus
Lilium longiflorum Trumpet lily
Lycopersicon esculentum Tomato
Malus domestica Apple
Manihot esculenta Cassava
Marchantia polymorpha
Medicago truncatula Barrel medic
Mesembryanthemum crystallinum Ice plant
Mucor circinelloides Fungus
Mucor racemosus Fungus
Neurospora crassa
Nicotiana tabacum Tobacco
Oryza sativa Rice
Petunia x hybrida
Phaseolus vulgaris Bean
Physcomitrella patens Moss
Pichia angusta
Pichia pastoris
Pinus strobus Eastern white pine
Pinus sylvestris Scots pine
Pinus taeda Loblolly pine
Pisum sativum Pea
Pleurotus ostreatus Oyster mushroom
Porphyra pulchra Red alga
Porphyra yezoensis Red alga
Prunus persica Peach
Ricinus communis Castor bean
Saccharomyces cerevisiae Baker's yeast
Schizosaccharomyces pombe Fission yeast
Sclerotinia sclerotiorum
Silene latifolia Bladder campion
Solanum tuberosum Potato
Sorghum bicolor Sorghum
Uncinula necator Powdery mildew fungus
Ustilago maydis
Vitis vinifera Grape vine
Zea mays Corn
Zinnia elegans Zinnia

Primates (gbpri):
Homo sapiens Human

Rodents (gbrod):
Cavia porcellus Guinea pig
Mus musculus Mouse
Rattus norvegicus Rat

Viruses (gbvrl):
Chilo iridescent virus CIV
grapevine leafroll-associated virus 2
Human herpesvirus 4

Vertebrates (gbvrt):
Ambystoma mexicanum Salamander
Anas platyrhynchos Mallard duck
Cairina moschata Muscovy duck
Danio rerio Zebra fish
Eptatretus stouti Pacific hagfish
Fugu rubripes Puffer fish
Gallus gallus Chicken
Myxine glutinosa Atlantic hagfish
Petromyzon marinus Sea lamprey
Platichthys flesus European flounder
Trachemys scripta Red-eared slider turtle
Squalus acanthias Spiny dogfish
Xenopus laevis African clawed frog


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