#EMBOSS codon usage tables
#
#Original EMBOSS tables were taken from:
#
# Mike Cherry's codonusage database 1992
#  ftp://ftp.ebi.ac.uk/pub/databases/codonusage
#
# Transterm database 1994
#  ftp://ftp.ebi.ac.uk/pub/databases/transterm
#
# and provided by the EMBOSS team for missing taxonomic groups
#
#Naming: bacteria are Egss
#        plants are 3 letter abbreviations etc.
#        animals are common names etc.
#        organelles are prefix ch or suffix mt/mit (make standard)
#
# Old files are now considered obsolete and are replaced as follows:
# File name       Species (Old name)
# =========       ==================

Eacica.cut       Acinetobacter_calcoaceticus (Eacc.cut)
Eagrtu.cut       Agrobacterium_tumefaciens_str__C58 (Eatu.cut)
Eanasp.cut       Anabaena_sp_ (Eanasp.cut)
Earath.cut       Arabidopsis_thaliana (Eath.cut)
Eazovi.cut       Azotobacter_vinelandii (Eazovi.cut)
Ebacme.cut       Bacillus_megaterium (Ebme.cut)
Ebacst.cut       Geobacillus_stearothermophilus (Ebst.cut)
Ebacsu.cut       Bacillus_subtilis (Ebsu.cut)
Ebacsu_high.cut  Bacillus_subtilis (high) (Ebsu_h.cut)
Ebommo.cut       Bombyx_mori (silkmoth) (Ebmo.cut)
Ebovin.cut       Bos_taurus (Ebov.cut)
Ebpphx.cut       Bacteriophage phi-X174 (Ephix174.cut)
Ebraja.cut       Bradyrhizobium_japonicum_USDA_110 (Ebja.cut)
Ebrana.cut       Brassica_napus (rape) (Ebna.cut)
Ebrare.cut       Brachydanio_rerio (zebrafish) (Ezebrafish.cut)
Ecaeel.cut       Caenorhabditis_elegans (nematode) (Ecel.cut)
Ecanal.cut       Candida_albicans (Ecal.cut)
Ecanfa.cut       Canis_familiaris (dog) (Edog.cut)
Ecaucr.cut       Caulobacter_crescentus_CB15 (Eccr.cut)
Echick.cut       Gallus_gallus (Echk.cut)
Echlre.cut       Chlamydomonas_reinhardtii (Ecre.cut)
Echltr.cut       Chlamydia_trachomatis_D_UW-3_CX (Ectr.cut)
Ecloab.cut       Clostridium_acetobutylicum_ATCC_824 (Ecac.cut)
Ecrigr.cut       Cricetulus_greseus (hamster) (Eham.cut)
Ecyapa.cut       Cyanophora_paradoxa (Ecpx.cut)
Edayhoff.cut  artificial ... needs stop codon frequency (Edayhoff.cut)
Edicdi.cut       Dictyostelium_discoideum (Eddi.cut)
Edicdi_high.cut  Dictyostelium_discoideum (high) (Eddi_h.cut)
Edrome.cut       Drosophila_melanogaster (Edro.cut)
Edrome_high.cut  Drosophila_melanogaster (high) (Edro_h.cut)
Eecoli.cut       Escherichia_coli_K12 (Eeco.cut)
Eecoli_high.cut  Escherichia_coli_K12 (high) (Eeco_h.cut)
Eemeni.cut       Emericella_nidulans (Eani.cut)
Eemeni_mit.cut   mitochondrion_Emericella_nidulans (Eanidmit.cut)
Eemeni_high.cut  Emericella_nidulans highly expressed (Eani_h.cut)
Eerwct.cut       Erwinia_carotovora_subsp__atroseptica_SCRI1043. (Eeca.cut)
Ehaein.cut       Haemophilus_influenzae_Rd_KW20 (Ehin.cut)
Ehalma.cut       Haloarcula_marismortui_ATCC_43049 (Halobacterium marismortui) (Ehma.cut)
Ehalsa.cut       Halobacterium_salinarum_NRC-1 (Halobacterium halobium) (Ehha.cut)
Ehorvu.cut       Hordeum_vulgare_subsp__vulgare (Barley) (Ebly.cut)
Ehuman.cut       Homo_sapiens (Ehum.cut)
Eklepn.cut       Klebsiella_pneumoniae (Ekpn.cut)
Eklula.cut       Kluyveromyces_lactis_NRRL_Y-1140 (Ekla.cut)
Elacdl.cut       Lactococcus_lactis_subsp__lactis_Il1403 L. delbrueckii subsp lactis (Ella.cut)
Elyces.cut       Lycopersicon_esculentum (tomato) (Etom.cut)
Emacfa.cut       Macaca_fascicularis (Emac.cut)
Emaize.cut       Zea_mays (Ezma.cut)
Emaize_chl.cut   chloroplast_Zea_mays (Echzm.cut)
Emammal_high.cut Mammalian species (high) (Emam_h.cut)
Emanse.cut       Manduca_sexta (Emse.cut)
Emarpo_chl.cut   chloroplast_Marchantia_polymorpha (liverwort) (Echmp.cut)
Emedsa.cut       Medicago_sativa (Emsa.cut)
Emetth.cut       Methanothermobacter_thermautotrophicus_str__Delta_H (Emta.cut)
Emouse.cut       Mus_musculus (mus.cutE)
Emyctu.cut       Mycobacterium_tuberculosis_H37Rv (Emtu.cut)
Eneigo.cut       Neisseria_gonorrhoeae (Engo.cut)
Eneucr.cut       Neurospora_crassa (Encr.cut)
Eoncmy.cut       Oncorhynchus_mykiss (rainbow trout) (Eoncsp.cut)
Eorysa.cut       Oryza_sativa (rice) (Eric.cut)
Eorysa_chl.cut   chloroplast_Oryza_sativa (Echos.cut)
Epea.cut         Pisum_sativum (pea) (Epea.cut)
Epethy.cut       Petunia_x_hybrida (Ephy.cut)
Ephavu.cut       Phaseolus_vulgaris (lima bean)(Ephv.cut)
Epig.cut         Sus_scrofa (pig) (Epig.cut)
Eplafa.cut       Plasmodium_falciparum_3D7 (Epfa.cut)
Eprovu.cut       Proteus_vulgaris. (Epvu.cut)
Epseae.cut       Pseudomonas_aeruginosa_PAO1 (Epae.cut)
Epsepu.cut       Pseudomonas_putida_KT2440 (Eppu.cut)
Epsesm.cut       Pseudomonas_syringae_pv__tomato_str__DC3000 (Epsy.cut)
Erabit.cut       Oryctolagus_cuniculus (rabbit) (Erab.cut)
Erat.cut         Rattus_norvegicus (Erat.cut)
Erhile.cut       Rhizobium_leguminosarum (Erle.cut)
Erhime.cut       Sinorhizobium_meliloti_1021 (Erhm.cut)
Erhoca.cut       Rhodobacter_capsulatus (Erca.cut)
Erhosh.cut       Rhodobacter_sphaeroides (Ersp.cut)
Esalsa.cut       Salmo_salar (Atlantic salmon) (Esalsp.cut)
Esalty.cut       Salmonella_typhimurium_LT2 (Esty.cut)
Eschma.cut       Schistosoma_mansoni (smi.cutE)
Eschpo.cut       Schizosaccharomyces_pombe (Espo.cut)
Eschpo_cai.cut   Schizosaccharomyces pombe (CAI equivalent) (Epombecai.cut)
Eschpo_high.cut  Schizosaccharomyces_pombe (high)(Espo_h.cut)
Eserma.cut       Serratia_marcescens (Esma.cut)
Esheep.cut       Ovis_aries (sheep) (Eshp.cut)
Esoltu.cut       Solanum_tuberosum (potato) (Epot.cut)
Esoybn.cut       Glycine_max (soybean) (Esoy.cut)
Espiol.cut       Spinacia_oleracea (spinach) (Espi.cut)
Estaau.cut       Staphylococcus_aureus (sau.cutE)
Estrco.cut       Streptomyces_coelicolor_A3_2_ (Esco.cut)
Estrmu.cut       Streptococcus_mutans_UA159 (Esmu.cut)
Estrpn.cut       Streptococcus_pneumoniae_R6 (Espn.cut)
Estrpu.cut       Strongylocentrotus_purpuratus (sea urchin) (Espu.cut)
Esv40.cut        Simian Virus 40 (Esv40.cut)
Esynco.cut       Synechococcus_sp__WH_8102 (Esynsp.cut)
Esyncy.cut       Synechocystis_sp__PCC_6803 (Esyhsp.cut)
Etetpy.cut       Tetrahymena_thermophila (Etetsp.cut)
Etheth.cut       Thermus_thermophilus_HB8 (Eter.cut) 
Etobac.cut       Nicotiana_tabacum (tobacco) (Etob.cut)
Etobac_chl.cut   chloroplast_Nicotiana_tabacum (Echnt.cut)
Etrybr.cut       Trypanosoma_brucei (Etbr.cut)
Etrycr.cut       Trypanosoma_cruzi (Etcr.cut)
Evibch.cut       Vibrio_cholerae_O1_biovar_eltor_str__N16961 (Evco.cut)
Ewheat.cut       Triticum_aestivum (wheat) (Ewht.cut)
Exenla.cut       Xenopus_laevis (Exel.cut)
Eyeast.cut      Saccharomyces_cerevisiae (Eyeast.cut)
Eyeast_cai.cut  Saccharomyces_cerevisiae original CAI set (Eyeastcai.cut)
Eyeast_high.cut Saccharomyces_cerevisiae (high) (Eysc_h.cut)
Eyeast_mit.cut  mitochondrion_Saccharomyces_cerevisiae (Eyscmt.cut)
Eyeren.cut      Yersinia_enterocolitica (Eyen.cut)
Eyerpe.cut      Yersinia pestis


#Missing species from the large CUTG files:
#
#Shigella flexneri (E) - see E.coli O157