# Interval data is stored here #data_dir = /Users/pcingola/snpEff/data/ data_dir = /seq/references/Homo_sapiens_assembly19/v1/snpEff/v2_0_5/data/ # Database repository: A URL to the server where you can download databases (command: 'snpEff download dbName') database_repository = http://sourceforge.net/projects/snpeff/files/databases # Store cache files here cache_dir = /seq/picardtemp3 #--- # Comma separated list of genomes # # Each genome version XX can have separate config file located in data_dir/XX/snpEff.config # For each genome 'XX' a set of attributes are defined # - XX.genome : # The name of this genome # - chromoName.codonTable : # Codon table for a chromosome in this genome (e.g. mithoncondrial codon table). #--- genomes : \ ailmel1.61 \ , agam \ , alyrata107, alyrata1 \ , amel2 \ , anoCar1.0.60 , anoCar2.0.61 \ , athaliana130, athalianaTair9, athalianaTair10 \ , aquiCoer \ , btau4.0.59 , btau4.0.60, btau4.0.61 \ , bushBaby1.60, bushBaby1.61 \ , cAlbicansv21 \ , calJac3.2.1.60, calJac3.2.1.61 \ , canFam2.59 , canFam2.60, canFam2.61 \ , cat1.60, cat1.61 \ , cavPor3.60, cavPor3.61 \ , ce.WS201, ce.WS210.60, ce.WS220.61 \ , chimp2.1.59 , chimp2.1.60, chimp2.1.61 \ , choHof1.60, choHof1.61 \ , cInt2.60, cInt2.61 \ , crubella \ , cSav2.0.60, cSav2.0.61 \ , danRer8.59 , danRer9.60, danRer9.61 \ , dasNov2.60, dasNov2.61 \ , dipOrd1.60, dipOrd1.61 \ , dm5.12 , dm5.22 , dm5.30 , dm5.31, dm5.32, dm5.34, dm5.40, dm5.42 \ , dm5.25.59 , dm5.25.60, dm5.25.61, dm5.25.63 \ , equCab2.60, equCab2.61 \ , eriEur1.60, eriEur1.61 \ , fugu4.60, fugu4.61 \ , gacu1.60, gacu1.61 \ , ggallus2.59 , ggallus2.60, ggallus2.61 \ , gmax1.09 \ , gorGor3.60, gorGor3.61 \ , hg36.54, hg19, hg37.59 , hg37.60, hg37.61, hg37.63 \ , hiv \ , loxAfr3.60, loxAfr3.61 \ , maizeZmB73 \ , medaka1.60, medaka1.61 \ , meug1.0.60, meug1.0.61 \ , micMur1.60, micMur1.61 \ , mm37 , mm37.59 , mm37.60, mm37.61 \ , mmul1.60, mmul1.61 \ , monDom5.60, monDom5.61 \ , myco_fh, myco_m129 \ , myoLuc1.60, myoLuc1.61 \ , ncrassa \ , NC_000913 \ , oana5.60, oana5.61 \ , ochPri2.60, ochPri2.61 \ , oryCun2.60, oryCun2.61 \ , pfluo.SBW25.NC_009444 \ , pfluo.SBW25.NC_012660 \ , paeru.PA01 \ , paeru.PA14 \ , peromyscus \ , plasmo72 \ , ppersica139 \ , ppyg2.60, ppyg2.61 \ , proCap1.60, proCap1.61 \ , pteVam1.60, pteVam1.61 \ , rat3.4.59 , rat3.4.60, rat3.4.61 \ , rice5, rice6.1 \ , sacCer2, sacCer2.59 , sacCer2.60, sacCer2.61 \ , SIVmac239 \ , sorAra1.60, sorAra1.61 \ , speTri1.60, speTri1.61 \ , spombe \ , sScrofa9.60, sScrofa9.61 \ , taeGut3.2.4.60, taeGut3.2.4.61 \ , tarSyr1.60, tarSyr1.61 \ , tenrec1.60, tenrec1.61 \ , testCase, testCaseHg, testHg3763Chr1, testHg3761Chr15, testHg3761Chr16, testHg3763Chr20, testHg3763ChrY, test, test_ENSG00000158062 \ , tetraodon8.60, tetraodon8.61 \ , tupBel1.60, tupBel1.61 \ , turTru1.60, turTru1.61 \ , turkey.UMD2.61 \ , UMD3_1 \ , vacwr \ , vibrio \ , vicPac1.60, vicPac1.61 \ , xtrop4.1.60, xtrop4.1.61, xtrop7.1 \ \ , ailMel1.63 \ , AnoCar2.0.63 \ , BDGP5.25.63 \ , BROADD2.63 \ , BROADO5.63 \ , BROADS1.63 \ , Btau_4.0.63 \ , BUSHBABY1.63 \ , CAT.63 \ , cavPor3.63 \ , CHIMP2.1.63 \ , choHof1.63 \ , C_jacchus3.2.1.63 \ , COMMON_SHREW1.63 \ , CSAV2.0.63 \ , dasNov2.63 \ , dipOrd1.63 \ , EF3.63 \ , EquCab2.63 \ , FUGU4.63 \ , gorGor3.63 \ , GRCh37.63 \ , HEDGEHOG.63 \ , JGI2.63 \ , JGI_4.2.63 \ , loxAfr3.63 \ , MEDAKA1.63 \ , Meug_1.0.63 \ , micMur1.63 \ , MMUL_1.63 \ , Myoluc2.0.63 \ , NCBIM37.63 \ , Nleu1.0.63 \ , OANA5.63 \ , oryCun2.63 \ , pika.63 \ , PPYG2.63 \ , proCap1.63 \ , pteVam1.63 \ , RGSC3.4.63 \ , SQUIRREL.63 \ , Sscrofa9.63 \ , taeGut3.2.4.63 \ , tarSyr1.63 \ , TENREC.63 \ , TETRAODON8.63 \ , TREESHREW.63 \ , turTru1.63 \ , UMD2.63 \ , vicPac1.63 \ , WASHUC2.63 \ , WS220.63 \ , Zv9.63 \ \ , ailMel1.64 \ , AnoCar2.0.64 \ , BDGP5.25.64 \ , BROADD2.64 \ , BROADO5.64 \ , BROADS1.64 \ , BUSHBABY1.64 \ , CAT.64 \ , cavPor3.64 \ , CHIMP2.1.64 \ , choHof1.64 \ , C_jacchus3.2.1.64 \ , COMMON_SHREW1.64 \ , CSAV2.0.64 \ , dasNov2.64 \ , DEVIL7.0.64 \ , dipOrd1.64 \ , EF3.64 \ , EquCab2.64 \ , FUGU4.64 \ , gorGor3.1.64 \ , GRCh37.64 \ , HEDGEHOG.64 \ , JGI2.64 \ , JGI_4.2.64 \ , loxAfr3.64 \ , MEDAKA1.64 \ , Meug_1.0.64 \ , micMur1.64 \ , MMUL_1.64 \ , Myoluc2.0.64 \ , NCBIM37.64 \ , Nleu1.0.64 \ , OANA5.64 \ , oryCun2.64 \ , Petromyzon_marinus_7.0.64 \ , pika.64 \ , PPYG2.64 \ , proCap1.64 \ , pteVam1.64 \ , RGSC3.4.64 \ , SQUIRREL.64 \ , Sscrofa9.64 \ , taeGut3.2.4.64 \ , tarSyr1.64 \ , TENREC.64 \ , TETRAODON8.64 \ , TREESHREW.64 \ , turTru1.64 \ , UMD2.64 \ , UMD3.1.64 \ , vicPac1.64 \ , WASHUC2.64 \ , WS220.64 \ , Zv9.64 \ \ , ailMel1.65 \ , AnoCar2.0.65 \ , BDGP5.25.65 \ , BROADD2.65 \ , BROADO5.65 \ , BROADS1.65 \ , BUSHBABY1.65 \ , CAT.65 \ , cavPor3.65 \ , CHIMP2.1.65 \ , choHof1.65 \ , C_jacchus3.2.1.65 \ , COMMON_SHREW1.65 \ , CSAV2.0.65 \ , dasNov2.65 \ , DEVIL7.0.65 \ , dipOrd1.65 \ , EF3.65 \ , EquCab2.65 \ , FUGU4.65 \ , gorGor3.1.65 \ , GRCh37.65 \ , HEDGEHOG.65 \ , JGI2.65 \ , JGI_4.2.65 \ , loxAfr3.65 \ , MEDAKA1.65 \ , Meug_1.0.65 \ , micMur1.65 \ , MMUL_1.65 \ , Myoluc2.0.65 \ , NCBIM37.65 \ , Nleu1.0.65 \ , OANA5.65 \ , oryCun2.65 \ , Petromyzon_marinus_7.0.65 \ , pika.65 \ , PPYG2.65 \ , proCap1.65 \ , pteVam1.65 \ , RGSC3.4.65 \ , SQUIRREL.65 \ , Sscrofa9.65 \ , taeGut3.2.4.65 \ , tarSyr1.65 \ , TENREC.65 \ , TETRAODON8.65 \ , TREESHREW.65 \ , turTru1.65 \ , UMD2.65 \ , UMD3.1.65 \ , vicPac1.65 \ , WASHUC2.65 \ , WS220.65 \ , Zv9.65 \ #--- # Codon tables # # Format: It's a comma separated "codon/aminoAcid[+*]" list # Where 'codon' is in uppper case, aminoAcid is a one letter coce, '+' denotes start codon and '*' denotes stop codon # # References: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi # ftp://ftp.ncbi.nih.gov/entrez/misc/data/gc.prt #--- codon.Standard: TTT/F, TTC/F, TTA/L, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G codon.Vertebrate_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/M+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/*, AGG/*, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G codon.Yeast_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/T, CTC/T, CTA/T, CTG/T, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/M+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G codon.Mold_Mitochondrial: TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G codon.Protozoan_Mitochondrial: TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G codon.Coelenterate: TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G codon.Mitochondrial: TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G codon.Mycoplasma: TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G codon.Spiroplasma: TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G codon.Invertebrate_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/M+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G codon.Ciliate_Nuclear: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/Q, TAG/Q, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G codon.Dasycladacean_Nuclear: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/Q, TAG/Q, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G codon.Hexamita_Nuclear: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/Q, TAG/Q, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G codon.Echinoderm_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/N, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G codon.Flatworm_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/N, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G codon.Euplotid_Nuclear: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/C, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G codon.Bacterial_and_Plant_Plastid: TTT/F, TTC/F, TTA/L, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G codon.Alternative_Yeast_Nuclear: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/S+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G codon.Ascidian_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/M+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/G, AGG/G, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G codon.Alternative_Flatworm_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/Y, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/N, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G codon.Blepharisma_Macronuclear: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/Q, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G codon.Chlorophycean_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/L, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G codon.Trematode_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/M, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/N, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G codon.Scenedesmus_obliquus_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/*, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/L, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G codon.Thraustochytrium_Mitochondrial: TTT/F, TTC/F, TTA/*, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G #--- # Genome details #--- # Ailuropoda_melanoleuca ailmel1.61.genome : Ailuropoda_melanoleuca # Anopheles_gambiae agam.genome : Anopheles_gambiae # Arabidopsis lyrata (107) . Reference: http://www.phytozome.net/search.php?method=Org_Alyrata alyrata107.genome : Arabidopsis_lyrata # Arabidopsis lyrata (1) . Reference: http://genome.jgi-psf.org/Araly1/Araly1.download.ftp.html alyrata1.genome : Arabidopsis_lyrata # Apis mellifera amel2.genome : Bee # Anolis carolinensis genes (AnoCar1.0) (ENSEMBL) anoCar1.0.60.genome : Anolis_carolinensis anoCar2.0.61.genome : Anolis_carolinensis # Aquilegia coerulea aquiCoer.genome : Aquilegia_coerulea # Arabidopsis Thaliana (130). Reference: http://www.phytozome.net/dataUsagePolicy.php?org=Org_Athaliana athaliana130.genome : Arabidopsis_Thaliana # Arabidopsis Thaliana (TAIR 9). # References: # ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR9_genome_release/TAIR9_gff3/TAIR9_GFF3_genes.gff # ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR9_genome_release/TAIR9_chr_all.fas athalianaTair9.genome : Arabidopsis_Thaliana # Arabidopsis Thaliana (TAIR 10). Reference: ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR10_genome_release athalianaTair10.genome : Arabidopsis_Thaliana # Bos taurus genes (Btau_4.0) (ENSEMBL) btau4.0.59.genome : Bos_taurus btau4.0.60.genome : Bos_taurus btau4.0.61.genome : Bos_taurus # Otolemur garnettii genes (otoGar1) (ENSEMBL) bushBaby1.60.genome : Otolemur_garnettii bushBaby1.61.genome : Otolemur_garnettii # Candida_albicans_SC5314 http://www.candidagenome.org/download/gff/C_albicans_SC5314/ cAlbicansv21.genome: Candida_albicans_SC5314 # Callithrix jacchus genes (calJac3) (ENSEMBL) calJac3.2.1.60.genome : Callithrix_jacchus calJac3.2.1.61.genome : Callithrix_jacchus # Canis familiaris genes (CanFam_2.0) (ENSEMBL) canFam2.59.genome : Canis_familiaris canFam2.60.genome : Canis_familiaris canFam2.61.genome : Canis_familiaris # Felis catus genes (CAT) (ENSEMBL) cat1.60.genome : Felis_catus cat1.61.genome : Felis_catus # Cavia porcellus genes (cavPor3) (ENSEMBL) cavPor3.60.genome : Cavia_porcellus cavPor3.61.genome : Cavia_porcellus # Caenorhabditis elegans genes (WS210) (ENSEMBL) ce.WS201.genome : Caenorhabditis_elegans ce.WS210.60.genome : Caenorhabditis_elegans ce.WS220.61.genome : Caenorhabditis_elegans # Pan troglodytes genes (CHIMP2.1) (ENSEMBL) chimp2.1.59.genome : Pan_troglodytes chimp2.1.60.genome : Pan_troglodytes chimp2.1.61.genome : Pan_troglodytes # Choloepus hoffmanni genes (choHof1) (ENSEMBL) choHof1.60.genome : Choloepus_hoffmanni choHof1.61.genome : Choloepus_hoffmanni # Ciona intestinalis genes (JGI2) (ENSEMBL) cInt2.60.genome : Ciona_intestinalis cInt2.61.genome : Ciona_intestinalis # Capsella_rubella_v1.0 (Toronto University, Grandiflora) crubella.genome : Capsella_rubella_v1.0 # Ciona savignyi genes (CSAV2.0) (ENSEMBL) cSav2.0.60.genome : Ciona_savignyi cSav2.0.61.genome : Ciona_savignyi # Danio rerio genes (Zv9) (ENSEMBL) danRer8.59.genome : Danio_rerio danRer9.60.genome : Danio_rerio danRer9.61.genome : Danio_rerio # Dasypus novemcinctus genes (dasNov2) (ENSEMBL) dasNov2.60.genome : Dasypus_novemcinctus dasNov2.61.genome : Dasypus_novemcinctus # Dipodomys ordii genes (dipOrd1) (ENSEMBL) dipOrd1.60.genome : Dipodomys_ordii dipOrd1.61.genome : Dipodomys_ordii # Drosophila melanogaster (ENSEMBL) dm5.25.59.genome : Drosophila_melanogaster dm5.25.60.genome : Drosophila_melanogaster dm5.25.61.genome : Drosophila_melanogaster dm5.25.63.genome : Drosophila_melanogaster # Drosophila melanogaster (FlyBase) dm5.12.genome : Drosophila_melanogaster dm5.22.genome : Drosophila_melanogaster dm5.30.genome : Drosophila_melanogaster dm5.31.genome : Drosophila_melanogaster dm5.32.genome : Drosophila_melanogaster dm5.34.genome : Drosophila_melanogaster dm5.40.genome : Drosophila_melanogaster dm5.42.genome : Drosophila_melanogaster # Equus caballus genes (EquCab2) (ENSEMBL) equCab2.60.genome : Equus_caballus equCab2.61.genome : Equus_caballus # Erinaceus europaeus genes (eriEur1) (ENSEMBL) eriEur1.60.genome : Erinaceus_europaeus eriEur1.61.genome : Erinaceus_europaeus # Takifugu rubripes genes (FUGU4.0) (ENSEMBL) fugu4.60.genome : Takifugu_rubripes fugu4.61.genome : Takifugu_rubripes # Gasterosteus aculeatus genes (BROADS1) (ENSEMBL) gacu1.60.genome : Gasterosteus_aculeatus gacu1.61.genome : Gasterosteus_aculeatus # Gallus gallus genes (WASHUC2) (ENSEMBL) ggallus2.59.genome : Gallus_gallus ggallus2.60.genome : Gallus_gallus ggallus2.61.genome : Gallus_gallus # Glycine max # Reference : ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v7.0/Gmax/ # Sequence : ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v7.0/Gmax/assembly/Gmax_109.fa.gz # Annotations : ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v7.0/Gmax/annotation/ gmax1.09.genome: Glycine_Max # Gorilla gorilla genes (gorGor3) (ENSEMBL) gorGor3.60.genome : Gorilla_gorilla gorGor3.61.genome : Gorilla_gorilla # Homo sapiens genes (GRCh37.p2) (ENSEMBL) hg36.54.genome : Homo_sapiens hg19.genome : Homo_sapiens hg37.59.genome : Homo_sapiens hg37.60.genome : Homo_sapiens hg37.61.genome : Homo_sapiens hg37.63.genome : Homo_sapiens # HIV_nc_001802_1 hiv.genome : hiv # Loxodonta africana genes (loxAfr3) (ENSEMBL) loxAfr3.60.genome : Loxodonta_africana loxAfr3.61.genome : Loxodonta_africana # Neurospora Crassa (reference http://www.broadinstitute.org/annotation/genome/neurospora/MultiDownloads.html) ncrassa.genome : Neurospora_Crassa # Ecoli K12 MG1655 NC_000913.genome : Escherichia_coli # Maize (http://ftp.maizesequence.org/) maizeZmB73.genome : Maize_ZmB73 # Oryzias latipes genes (HdrR) (ENSEMBL) medaka1.60.genome : Oryzias_latipes medaka1.61.genome : Oryzias_latipes # Macropus eugenii genes (Meug_1.0) (ENSEMBL) meug1.0.60.genome : Macropus_eugenii meug1.0.61.genome : Macropus_eugenii # Microcebus murinus genes (micMur1) (ENSEMBL) micMur1.60.genome : Microcebus_murinus micMur1.61.genome : Microcebus_murinus # Mus musculus genes (NCBIM37) (ENSEMBL) mm37.genome : Mus_musculus mm37.59.genome : Mus_musculus mm37.60.genome : Mus_musculus mm37.61.genome : Mus_musculus # Macaca mulatta genes (MMUL_1.0) (ENSEMBL) mmul1.60.genome : Macaca_mulatta mmul1.61.genome : Macaca_mulatta # Monodelphis domestica genes (monDom5) (ENSEMBL) monDom5.60.genome : Monodelphis_domestica monDom5.61.genome : Monodelphis_domestica # Mycoplasma pneumoninae FH myco_fh.genome : Mycoplasma_pneumoninae_FH # Mycoplasma pneumoninae M129 myco_m129.genome : Mycoplasma_pneumoninae_M129 # Myotis lucifugus genes (myoLuc1) (ENSEMBL) myoLuc1.60.genome : Myotis_lucifugus myoLuc1.61.genome : Myotis_lucifugus # Ornithorhynchus anatinus genes (OANA5) (ENSEMBL) oana5.60.genome : Ornithorhynchus_anatinus oana5.61.genome : Ornithorhynchus_anatinus # Ochotona princeps genes (OchPri2.0) (ENSEMBL) ochPri2.60.genome : Ochotona_princeps ochPri2.61.genome : Ochotona_princeps # Oryctolagus cuniculus genes (oryCun2.0) (ENSEMBL) oryCun2.60.genome : Oryctolagus_cuniculus oryCun2.61.genome : Oryctolagus_cuniculus # Pseudomonas aeruginosa, N_008463 paeru.PA01.genome : Pseudomonas_aeruginosa paeru.PA01.chromosomes : NC_002516.2 paeru.PA01.NC_002516.2.codonTable: Bacterial_and_Plant_Plastid # Pseudomonas aeruginosa, N_008463 paeru.PA14.genome : Pseudomonas_aeruginosa paeru.PA14.chromosomes : NC_008463.1 paeru.PA14.NC_008463.1.codonTable: Bacterial_and_Plant_Plastid # Peromyscus leucopus (white footed deer mice) peromyscus.genome : Peromyscus leucopus # Plasmodium falciparum (http://plasmodb.org/common/downloads/release-7.2/Pfalciparum/) plasmo72.genome: Plasmodium_falciparum # Peach (Prunus persica). Reference: ftp://ftp.plantgdb.org/download/Genomes/PeGDB/ ppersica139.genome : Peach # Pseudomonas fluorescens pfluo.SBW25.NC_009444.genome : Pseudomonas_fluorescens pfluo.SBW25.NC_009444.chromosomes : NC_009444.1 pfluo.SBW25.NC_009444.NC_009444.1.codonTable: Bacterial_and_Plant_Plastid # Pseudomonas fluorescens pfluo.SBW25.NC_012660.genome : Pseudomonas_fluorescens pfluo.SBW25.NC_012660.chromosomes : NC_012660.1 pfluo.SBW25.NC_012660.NC_012660.1.codonTable: Bacterial_and_Plant_Plastid # Pongo pygmaeus abelii genes (PPYG2) (ENSEMBL) ppyg2.60.genome : Pongo_pygmaeus ppyg2.61.genome : Pongo_pygmaeus # Procavia capensis genes (proCap1) (ENSEMBL) proCap1.60.genome : Procavia_capensis proCap1.61.genome : Procavia_capensis # Pteropus vampyrus genes (pteVam1) (ENSEMBL) pteVam1.60.genome : Pteropus_vampyrus pteVam1.61.genome : Pteropus_vampyrus # Rattus norvegicus genes (RGSC3.4) (ENSEMBL) rat3.4.59.genome : Rattus_norvegicus rat3.4.60.genome : Rattus_norvegicus rat3.4.61.genome : Rattus_norvegicus # Rice: http://rapdb.dna.affrc.go.jp/download/index.html rice5.genome: Rice_v5 # Rice: ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/ rice6.1.genome: Rice_v6_1 # Saccharomyces cerevisiae genes (SGD1.01) (ENSEMBL) sacCer2.genome : Saccharomyces_cerevisiae sacCer2.59.genome : Saccharomyces_cerevisiae sacCer2.60.genome : Saccharomyces_cerevisiae sacCer2.61.genome : Saccharomyces_cerevisiae # HIV virus (SIVmac239, http://www.ncbi.nlm.nih.gov/nuccore/334647) SIVmac239.genome : HIV # Sorex araneus genes (sorAra1) (ENSEMBL) sorAra1.60.genome : Sorex_araneus sorAra1.61.genome : Sorex_araneus # Spermophilus tridecemlineatus genes (speTri1) (ENSEMBL) speTri1.60.genome : Spermophilus_tridecemlineatus speTri1.61.genome : Spermophilus_tridecemlineatus # Schizosaccharomyces pombe (fission yeast). # References: # ftp://ftp.sanger.ac.uk/pub/yeast/pombe/GFF/pombe_09052011.gff # ftp://ftp.sanger.ac.uk/pub/yeast/pombe/GFF/pombe_09052011.fasta spombe.genome : Schizosaccharomyces_pombe # Sus scrofa genes (Sscrofa9) (ENSEMBL) sScrofa9.60.genome : Sus_scrofa sScrofa9.61.genome : Sus_scrofa # Taeniopygia guttata genes (taeGut3.2.4) (ENSEMBL) taeGut3.2.4.60.genome : Taeniopygia_guttata taeGut3.2.4.61.genome : Taeniopygia_guttata # Tarsius syrichta genes (tarSyr1) (ENSEMBL) tarSyr1.60.genome : Tarsius_syrichta tarSyr1.61.genome : Tarsius_syrichta # Echinops telfairi genes (TENREC) (ENSEMBL) tenrec1.60.genome : Echinops_telfairi tenrec1.61.genome : Echinops_telfairi # Used for debugging test.genome : test testHg3761Chr15.genome : Human_Chr15 testHg3761Chr16.genome : Human_Chr16 testHg3763Chr1.genome : Human_Chr1 testHg3763Chr20.genome : Human_Chr20 testHg3763ChrY.genome : Human_ChrY testCase.genome : Human testCaseHg.chromosomes: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y test_ENSG00000158062.genome : Human_Chr1_ENSG00000158062 # Tetraodon nigroviridis genes (TETRAODON8.0) (ENSEMBL) tetraodon8.60.genome : Tetraodon_nigroviridis tetraodon8.61.genome : Tetraodon_nigroviridis # Tupaia belangeri genes (tupBel1) (ENSEMBL) tupBel1.60.genome : Tupaia_belangeri tupBel1.61.genome : Tupaia_belangeri # Meleagris_gallopavo (Turkey) turkey.UMD2.61.genome : Meleagris_gallopavo # Tursiops truncatus genes (turTru1) (ENSEMBL) turTru1.60.genome : Tursiops_truncatus turTru1.61.genome : Tursiops_truncatus # Bos taurus : University of Maryland version 3.1 UMD3_1.genome : Bos_taurus # Vaccinia WR (NCBIM37) (ENSEMBL) gi|29692106|gb|AY243312.1| vacwr.genome : Vaccinia_Western_Reserve # Vibrio Cholerae vibrio.genome : Vibrio Cholerae vibrio.chromosomes : NC_002505.1, NC_002506.1 vibrio.NC_002505.1.codonTable : Bacterial_and_Plant_Plastid vibrio.NC_002506.1.codonTable : Bacterial_and_Plant_Plastid # Vicugna pacos genes (vicPac1) (ENSEMBL) vicPac1.60.genome : Vicugna_pacos vicPac1.61.genome : Vicugna_pacos # Xenopus tropicalis genes (JGI4.1)] (ENSEMBL) xtrop4.1.60.genome : Xenopus_tropicalis xtrop4.1.61.genome : Xenopus_tropicalis # Xenopus tropicalis ftp://ftp.xenbase.org/pub/Genomics/JGI/Xentr7.1/ xtrop7.1.genome : Xenopus_tropicalis #------------------------------------------------------------------------------- # Ensembl 63 versions #------------------------------------------------------------------------------- # ENSEMBL v63 : Ailuropoda_melanoleuca.ailMel1.63 ailMel1.63.genome : Ailuropoda_melanoleuca.ailMel1.63 # ENSEMBL v63 : Anolis_carolinensis.AnoCar2.0.63 AnoCar2.0.63.genome : Anolis_carolinensis.AnoCar2.0.63 # ENSEMBL v63 : Bos_taurus.Btau_4.0.63 Btau_4.0.63.genome : Bos_taurus.Btau_4.0.63 # ENSEMBL v63 : Caenorhabditis_elegans.WS220.63 WS220.63.genome : Caenorhabditis_elegans.WS220.63 # ENSEMBL v63 : Callithrix_jacchus.C_jacchus3.2.1.63 C_jacchus3.2.1.63.genome : Callithrix_jacchus.C_jacchus3.2.1.63 # ENSEMBL v63 : Canis_familiaris.BROADD2.63 BROADD2.63.genome : Canis_familiaris.BROADD2.63 # ENSEMBL v63 : Cavia_porcellus.cavPor3.63 cavPor3.63.genome : Cavia_porcellus.cavPor3.63 # ENSEMBL v63 : Choloepus_hoffmanni.choHof1.63 choHof1.63.genome : Choloepus_hoffmanni.choHof1.63 # ENSEMBL v63 : Ciona_intestinalis.JGI2.63 JGI2.63.genome : Ciona_intestinalis.JGI2.63 # ENSEMBL v63 : Ciona_savignyi.CSAV2.0.63 CSAV2.0.63.genome : Ciona_savignyi.CSAV2.0.63 # ENSEMBL v63 : Danio_rerio.Zv9.63 Zv9.63.genome : Danio_rerio.Zv9.63 # ENSEMBL v63 : Dasypus_novemcinctus.dasNov2.63 dasNov2.63.genome : Dasypus_novemcinctus.dasNov2.63 # ENSEMBL v63 : Dipodomys_ordii.dipOrd1.63 dipOrd1.63.genome : Dipodomys_ordii.dipOrd1.63 # ENSEMBL v63 : Drosophila_melanogaster.BDGP5.25.63 BDGP5.25.63.genome : Drosophila_melanogaster.BDGP5.25.63 # ENSEMBL v63 : Echinops_telfairi.TENREC.63 TENREC.63.genome : Echinops_telfairi.TENREC.63 # ENSEMBL v63 : Equus_caballus.EquCab2.63 EquCab2.63.genome : Equus_caballus.EquCab2.63 # ENSEMBL v63 : Erinaceus_europaeus.HEDGEHOG.63 HEDGEHOG.63.genome : Erinaceus_europaeus.HEDGEHOG.63 # ENSEMBL v63 : Felis_catus.CAT.63 CAT.63.genome : Felis_catus.CAT.63 # ENSEMBL v63 : Gallus_gallus.WASHUC2.63 WASHUC2.63.genome : Gallus_gallus.WASHUC2.63 # ENSEMBL v63 : Gasterosteus_aculeatus.BROADS1.63 BROADS1.63.genome : Gasterosteus_aculeatus.BROADS1.63 # ENSEMBL v63 : Gorilla_gorilla.gorGor3.63 gorGor3.63.genome : Gorilla_gorilla.gorGor3.63 # ENSEMBL v63 : Homo_sapiens.GRCh37.63 GRCh37.63.genome : Homo_sapiens.GRCh37.63 # ENSEMBL v63 : Loxodonta_africana.loxAfr3.63 loxAfr3.63.genome : Loxodonta_africana.loxAfr3.63 # ENSEMBL v63 : Macaca_mulatta.MMUL_1.63 MMUL_1.63.genome : Macaca_mulatta.MMUL_1.63 # ENSEMBL v63 : Macropus_eugenii.Meug_1.0.63 Meug_1.0.63.genome : Macropus_eugenii.Meug_1.0.63 # ENSEMBL v63 : Meleagris_gallopavo.UMD2.63 UMD2.63.genome : Meleagris_gallopavo.UMD2.63 # ENSEMBL v63 : Microcebus_murinus.micMur1.63 micMur1.63.genome : Microcebus_murinus.micMur1.63 # ENSEMBL v63 : Monodelphis_domestica.BROADO5.63 BROADO5.63.genome : Monodelphis_domestica.BROADO5.63 # ENSEMBL v63 : Mus_musculus.NCBIM37.63 NCBIM37.63.genome : Mus_musculus.NCBIM37.63 # ENSEMBL v63 : Myotis_lucifugus.Myoluc2.0.63 Myoluc2.0.63.genome : Myotis_lucifugus.Myoluc2.0.63 # ENSEMBL v63 : Nomascus_leucogenys.Nleu1.0.63 Nleu1.0.63.genome : Nomascus_leucogenys.Nleu1.0.63 # ENSEMBL v63 : Ochotona_princeps.pika.63 pika.63.genome : Ochotona_princeps.pika.63 # ENSEMBL v63 : Ornithorhynchus_anatinus.OANA5.63 OANA5.63.genome : Ornithorhynchus_anatinus.OANA5.63 # ENSEMBL v63 : Oryctolagus_cuniculus.oryCun2.63 oryCun2.63.genome : Oryctolagus_cuniculus.oryCun2.63 # ENSEMBL v63 : Oryzias_latipes.MEDAKA1.63 MEDAKA1.63.genome : Oryzias_latipes.MEDAKA1.63 # ENSEMBL v63 : Otolemur_garnettii.BUSHBABY1.63 BUSHBABY1.63.genome : Otolemur_garnettii.BUSHBABY1.63 # ENSEMBL v63 : Pan_troglodytes.CHIMP2.1.63 CHIMP2.1.63.genome : Pan_troglodytes.CHIMP2.1.63 # ENSEMBL v63 : Pongo_abelii.PPYG2.63 PPYG2.63.genome : Pongo_abelii.PPYG2.63 # ENSEMBL v63 : Procavia_capensis.proCap1.63 proCap1.63.genome : Procavia_capensis.proCap1.63 # ENSEMBL v63 : Pteropus_vampyrus.pteVam1.63 pteVam1.63.genome : Pteropus_vampyrus.pteVam1.63 # ENSEMBL v63 : Rattus_norvegicus.RGSC3.4.63 RGSC3.4.63.genome : Rattus_norvegicus.RGSC3.4.63 # ENSEMBL v63 : Saccharomyces_cerevisiae.EF3.63 EF3.63.genome : Saccharomyces_cerevisiae.EF3.63 # ENSEMBL v63 : Sorex_araneus.COMMON_SHREW1.63 COMMON_SHREW1.63.genome : Sorex_araneus.COMMON_SHREW1.63 # ENSEMBL v63 : Spermophilus_tridecemlineatus.SQUIRREL.63 SQUIRREL.63.genome : Spermophilus_tridecemlineatus.SQUIRREL.63 # ENSEMBL v63 : Sus_scrofa.Sscrofa9.63 Sscrofa9.63.genome : Sus_scrofa.Sscrofa9.63 # ENSEMBL v63 : Taeniopygia_guttata.taeGut3.2.4.63 taeGut3.2.4.63.genome : Taeniopygia_guttata.taeGut3.2.4.63 # ENSEMBL v63 : Takifugu_rubripes.FUGU4.63 FUGU4.63.genome : Takifugu_rubripes.FUGU4.63 # ENSEMBL v63 : Tarsius_syrichta.tarSyr1.63 tarSyr1.63.genome : Tarsius_syrichta.tarSyr1.63 # ENSEMBL v63 : Tetraodon_nigroviridis.TETRAODON8.63 TETRAODON8.63.genome : Tetraodon_nigroviridis.TETRAODON8.63 # ENSEMBL v63 : Tupaia_belangeri.TREESHREW.63 TREESHREW.63.genome : Tupaia_belangeri.TREESHREW.63 # ENSEMBL v63 : Tursiops_truncatus.turTru1.63 turTru1.63.genome : Tursiops_truncatus.turTru1.63 # ENSEMBL v63 : Vicugna_pacos.vicPac1.63 vicPac1.63.genome : Vicugna_pacos.vicPac1.63 # ENSEMBL v63 : Xenopus_tropicalis.JGI_4.2.63 JGI_4.2.63.genome : Xenopus_tropicalis.JGI_4.2.63 #------------------------------------------------------------------------------- # Ensembl 64 versions #------------------------------------------------------------------------------- # ENSEMBL v64 : Ailuropoda_melanoleuca.ailMel1.64 ailMel1.64.genome : Ailuropoda_melanoleuca # ENSEMBL v64 : Anolis_carolinensis.AnoCar2.0.64 AnoCar2.0.64.genome : Anolis_carolinensis # ENSEMBL v64 : Bos_taurus.UMD3.1.64 UMD3.1.64.genome : Bos_taurus # ENSEMBL v64 : Caenorhabditis_elegans.WS220.64 WS220.64.genome : Caenorhabditis_elegans # ENSEMBL v64 : Callithrix_jacchus.C_jacchus3.2.1.64 C_jacchus3.2.1.64.genome : Callithrix_jacchus # ENSEMBL v64 : Canis_familiaris.BROADD2.64 BROADD2.64.genome : Canis_familiaris # ENSEMBL v64 : Cavia_porcellus.cavPor3.64 cavPor3.64.genome : Cavia_porcellus # ENSEMBL v64 : Choloepus_hoffmanni.choHof1.64 choHof1.64.genome : Choloepus_hoffmanni # ENSEMBL v64 : Ciona_intestinalis.JGI2.64 JGI2.64.genome : Ciona_intestinalis # ENSEMBL v64 : Ciona_savignyi.CSAV2.0.64 CSAV2.0.64.genome : Ciona_savignyi # ENSEMBL v64 : Danio_rerio.Zv9.64 Zv9.64.genome : Danio_rerio # ENSEMBL v64 : Dasypus_novemcinctus.dasNov2.64 dasNov2.64.genome : Dasypus_novemcinctus # ENSEMBL v64 : Dipodomys_ordii.dipOrd1.64 dipOrd1.64.genome : Dipodomys_ordii # ENSEMBL v64 : Drosophila_melanogaster.BDGP5.25.64 BDGP5.25.64.genome : Drosophila_melanogaster # ENSEMBL v64 : Echinops_telfairi.TENREC.64 TENREC.64.genome : Echinops_telfairi # ENSEMBL v64 : Equus_caballus.EquCab2.64 EquCab2.64.genome : Equus_caballus # ENSEMBL v64 : Erinaceus_europaeus.HEDGEHOG.64 HEDGEHOG.64.genome : Erinaceus_europaeus # ENSEMBL v64 : Felis_catus.CAT.64 CAT.64.genome : Felis_catus # ENSEMBL v64 : Gallus_gallus.WASHUC2.64 WASHUC2.64.genome : Gallus_gallus # ENSEMBL v64 : Gasterosteus_aculeatus.BROADS1.64 BROADS1.64.genome : Gasterosteus_aculeatus # ENSEMBL v64 : Gorilla_gorilla.gorGor3.1.64 gorGor3.1.64.genome : Gorilla_gorilla # ENSEMBL v64 : Homo_sapiens.GRCh37.64 GRCh37.64.genome : Homo_sapiens # ENSEMBL v64 : Loxodonta_africana.loxAfr3.64 loxAfr3.64.genome : Loxodonta_africana # ENSEMBL v64 : Macaca_mulatta.MMUL_1.64 MMUL_1.64.genome : Macaca_mulatta # ENSEMBL v64 : Macropus_eugenii.Meug_1.0.64 Meug_1.0.64.genome : Macropus_eugenii # ENSEMBL v64 : Meleagris_gallopavo.UMD2.64 UMD2.64.genome : Meleagris_gallopavo # ENSEMBL v64 : Microcebus_murinus.micMur1.64 micMur1.64.genome : Microcebus_murinus # ENSEMBL v64 : Monodelphis_domestica.BROADO5.64 BROADO5.64.genome : Monodelphis_domestica # ENSEMBL v64 : Mus_musculus.NCBIM37.64 NCBIM37.64.genome : Mus_musculus # ENSEMBL v64 : Myotis_lucifugus.Myoluc2.0.64 Myoluc2.0.64.genome : Myotis_lucifugus # ENSEMBL v64 : Nomascus_leucogenys.Nleu1.0.64 Nleu1.0.64.genome : Nomascus_leucogenys # ENSEMBL v64 : Ochotona_princeps.pika.64 pika.64.genome : Ochotona_princeps # ENSEMBL v64 : Ornithorhynchus_anatinus.OANA5.64 OANA5.64.genome : Ornithorhynchus_anatinus # ENSEMBL v64 : Oryctolagus_cuniculus.oryCun2.64 oryCun2.64.genome : Oryctolagus_cuniculus # ENSEMBL v64 : Oryzias_latipes.MEDAKA1.64 MEDAKA1.64.genome : Oryzias_latipes # ENSEMBL v64 : Otolemur_garnettii.BUSHBABY1.64 BUSHBABY1.64.genome : Otolemur_garnettii # ENSEMBL v64 : Pan_troglodytes.CHIMP2.1.64 CHIMP2.1.64.genome : Pan_troglodytes # ENSEMBL v64 : Petromyzon_marinus.Petromyzon_marinus_7.0.64 Petromyzon_marinus_7.0.64.genome : Petromyzon_marinus # ENSEMBL v64 : Pongo_abelii.PPYG2.64 PPYG2.64.genome : Pongo_abelii # ENSEMBL v64 : Procavia_capensis.proCap1.64 proCap1.64.genome : Procavia_capensis # ENSEMBL v64 : Pteropus_vampyrus.pteVam1.64 pteVam1.64.genome : Pteropus_vampyrus # ENSEMBL v64 : Rattus_norvegicus.RGSC3.4.64 RGSC3.4.64.genome : Rattus_norvegicus # ENSEMBL v64 : Saccharomyces_cerevisiae.EF3.64 EF3.64.genome : Saccharomyces_cerevisiae # ENSEMBL v64 : Sarcophilus_harrisii.DEVIL7.0.64 DEVIL7.0.64.genome : Sarcophilus_harrisii # ENSEMBL v64 : Sorex_araneus.COMMON_SHREW1.64 COMMON_SHREW1.64.genome : Sorex_araneus # ENSEMBL v64 : Spermophilus_tridecemlineatus.SQUIRREL.64 SQUIRREL.64.genome : Spermophilus_tridecemlineatus # ENSEMBL v64 : Sus_scrofa.Sscrofa9.64 Sscrofa9.64.genome : Sus_scrofa # ENSEMBL v64 : Taeniopygia_guttata.taeGut3.2.4.64 taeGut3.2.4.64.genome : Taeniopygia_guttata # ENSEMBL v64 : Takifugu_rubripes.FUGU4.64 FUGU4.64.genome : Takifugu_rubripes # ENSEMBL v64 : Tarsius_syrichta.tarSyr1.64 tarSyr1.64.genome : Tarsius_syrichta # ENSEMBL v64 : Tetraodon_nigroviridis.TETRAODON8.64 TETRAODON8.64.genome : Tetraodon_nigroviridis # ENSEMBL v64 : Tupaia_belangeri.TREESHREW.64 TREESHREW.64.genome : Tupaia_belangeri # ENSEMBL v64 : Tursiops_truncatus.turTru1.64 turTru1.64.genome : Tursiops_truncatus # ENSEMBL v64 : Vicugna_pacos.vicPac1.64 vicPac1.64.genome : Vicugna_pacos # ENSEMBL v64 : Xenopus_tropicalis.JGI_4.2.64 JGI_4.2.64.genome : Xenopus_tropicalis #------------------------------------------------------------------------------- # Ensembl 65 versions #------------------------------------------------------------------------------- # ENSEMBL v65 : Ailuropoda_melanoleuca.ailMel1.65 ailMel1.65.genome : Ailuropoda_melanoleuca # ENSEMBL v65 : Anolis_carolinensis.AnoCar2.0.65 AnoCar2.0.65.genome : Anolis_carolinensis # ENSEMBL v65 : Bos_taurus.UMD3.1.65 UMD3.1.65.genome : Bos_taurus # ENSEMBL v65 : Caenorhabditis_elegans.WS220.65 WS220.65.genome : Caenorhabditis_elegans # ENSEMBL v65 : Callithrix_jacchus.C_jacchus3.2.1.65 C_jacchus3.2.1.65.genome : Callithrix_jacchus # ENSEMBL v65 : Canis_familiaris.BROADD2.65 BROADD2.65.genome : Canis_familiaris # ENSEMBL v65 : Cavia_porcellus.cavPor3.65 cavPor3.65.genome : Cavia_porcellus # ENSEMBL v65 : Choloepus_hoffmanni.choHof1.65 choHof1.65.genome : Choloepus_hoffmanni # ENSEMBL v65 : Ciona_intestinalis.JGI2.65 JGI2.65.genome : Ciona_intestinalis # ENSEMBL v65 : Ciona_savignyi.CSAV2.0.65 CSAV2.0.65.genome : Ciona_savignyi # ENSEMBL v65 : Danio_rerio.Zv9.65 Zv9.65.genome : Danio_rerio # ENSEMBL v65 : Dasypus_novemcinctus.dasNov2.65 dasNov2.65.genome : Dasypus_novemcinctus # ENSEMBL v65 : Dipodomys_ordii.dipOrd1.65 dipOrd1.65.genome : Dipodomys_ordii # ENSEMBL v65 : Drosophila_melanogaster.BDGP5.25.65 BDGP5.25.65.genome : Drosophila_melanogaster # ENSEMBL v65 : Echinops_telfairi.TENREC.65 TENREC.65.genome : Echinops_telfairi # ENSEMBL v65 : Equus_caballus.EquCab2.65 EquCab2.65.genome : Equus_caballus # ENSEMBL v65 : Erinaceus_europaeus.HEDGEHOG.65 HEDGEHOG.65.genome : Erinaceus_europaeus # ENSEMBL v65 : Felis_catus.CAT.65 CAT.65.genome : Felis_catus # ENSEMBL v65 : Gallus_gallus.WASHUC2.65 WASHUC2.65.genome : Gallus_gallus # ENSEMBL v65 : Gasterosteus_aculeatus.BROADS1.65 BROADS1.65.genome : Gasterosteus_aculeatus # ENSEMBL v65 : Gorilla_gorilla.gorGor3.1.65 gorGor3.1.65.genome : Gorilla_gorilla # ENSEMBL v65 : Homo_sapiens.GRCh37.65 GRCh37.65.genome : Homo_sapiens # ENSEMBL v65 : Loxodonta_africana.loxAfr3.65 loxAfr3.65.genome : Loxodonta_africana # ENSEMBL v65 : Macaca_mulatta.MMUL_1.65 MMUL_1.65.genome : Macaca_mulatta # ENSEMBL v65 : Macropus_eugenii.Meug_1.0.65 Meug_1.0.65.genome : Macropus_eugenii # ENSEMBL v65 : Meleagris_gallopavo.UMD2.65 UMD2.65.genome : Meleagris_gallopavo # ENSEMBL v65 : Microcebus_murinus.micMur1.65 micMur1.65.genome : Microcebus_murinus # ENSEMBL v65 : Monodelphis_domestica.BROADO5.65 BROADO5.65.genome : Monodelphis_domestica # ENSEMBL v65 : Mus_musculus.NCBIM37.65 NCBIM37.65.genome : Mus_musculus # ENSEMBL v65 : Myotis_lucifugus.Myoluc2.0.65 Myoluc2.0.65.genome : Myotis_lucifugus # ENSEMBL v65 : Nomascus_leucogenys.Nleu1.0.65 Nleu1.0.65.genome : Nomascus_leucogenys # ENSEMBL v65 : Ochotona_princeps.pika.65 pika.65.genome : Ochotona_princeps # ENSEMBL v65 : Ornithorhynchus_anatinus.OANA5.65 OANA5.65.genome : Ornithorhynchus_anatinus # ENSEMBL v65 : Oryctolagus_cuniculus.oryCun2.65 oryCun2.65.genome : Oryctolagus_cuniculus # ENSEMBL v65 : Oryzias_latipes.MEDAKA1.65 MEDAKA1.65.genome : Oryzias_latipes # ENSEMBL v65 : Otolemur_garnettii.BUSHBABY1.65 BUSHBABY1.65.genome : Otolemur_garnettii # ENSEMBL v65 : Pan_troglodytes.CHIMP2.1.65 CHIMP2.1.65.genome : Pan_troglodytes # ENSEMBL v65 : Petromyzon_marinus.Petromyzon_marinus_7.0.65 Petromyzon_marinus_7.0.65.genome : Petromyzon_marinus # ENSEMBL v65 : Pongo_abelii.PPYG2.65 PPYG2.65.genome : Pongo_abelii # ENSEMBL v65 : Procavia_capensis.proCap1.65 proCap1.65.genome : Procavia_capensis # ENSEMBL v65 : Pteropus_vampyrus.pteVam1.65 pteVam1.65.genome : Pteropus_vampyrus # ENSEMBL v65 : Rattus_norvegicus.RGSC3.4.65 RGSC3.4.65.genome : Rattus_norvegicus # ENSEMBL v65 : Saccharomyces_cerevisiae.EF3.65 EF3.65.genome : Saccharomyces_cerevisiae # ENSEMBL v65 : Sarcophilus_harrisii.DEVIL7.0.65 DEVIL7.0.65.genome : Sarcophilus_harrisii # ENSEMBL v65 : Sorex_araneus.COMMON_SHREW1.65 COMMON_SHREW1.65.genome : Sorex_araneus # ENSEMBL v65 : Spermophilus_tridecemlineatus.SQUIRREL.65 SQUIRREL.65.genome : Spermophilus_tridecemlineatus # ENSEMBL v65 : Sus_scrofa.Sscrofa9.65 Sscrofa9.65.genome : Sus_scrofa # ENSEMBL v65 : Taeniopygia_guttata.taeGut3.2.4.65 taeGut3.2.4.65.genome : Taeniopygia_guttata # ENSEMBL v65 : Takifugu_rubripes.FUGU4.65 FUGU4.65.genome : Takifugu_rubripes # ENSEMBL v65 : Tarsius_syrichta.tarSyr1.65 tarSyr1.65.genome : Tarsius_syrichta # ENSEMBL v65 : Tetraodon_nigroviridis.TETRAODON8.65 TETRAODON8.65.genome : Tetraodon_nigroviridis # ENSEMBL v65 : Tupaia_belangeri.TREESHREW.65 TREESHREW.65.genome : Tupaia_belangeri # ENSEMBL v65 : Tursiops_truncatus.turTru1.65 turTru1.65.genome : Tursiops_truncatus # ENSEMBL v65 : Vicugna_pacos.vicPac1.65 vicPac1.65.genome : Vicugna_pacos # ENSEMBL v65 : Xenopus_tropicalis.JGI_4.2.65 JGI_4.2.65.genome : Xenopus_tropicalis