Model Collections

Models and Model Collections

Models and model collections are organized on the taxonomic tree. Collections are anchored in the tree at the point of the common parent of all models in the collection. Branches of the tree that do not have side-branches are partially collapsed.

cellular organisms
- Bacteria
  - Pseudomonadati
    
    Pseudomonadota ∙ Gammaproteobacteria
    
    Enterobacterales
    
    Enterobacteriaceae
    
    Escherichia ∙ Escherichia coli
    
    Escherichia coli APEC O1
    
    iAPECO1_1312 Escherichia coli APEC O1
    
    Escherichia coli K-12
    
    Escherichia coli str. K-12 substr. W3110
    
    iY75_1357 Escherichia coli str. K-12 substr. W3110
    
    Escherichia coli str. K-12 substr. MG1655
    
    iJO1366 Escherichia coli str. K-12 substr. MG1655
    
    iAF1260 Escherichia coli str. K-12 substr. MG1655
    
    iML1515 Escherichia coli str. K-12 substr. MG1655
    
    iJR904 Escherichia coli str. K-12 substr. MG1655
    
    e_coli_core Escherichia coli str. K-12 substr. MG1655
    
    iAF1260b Escherichia coli str. K-12 substr. MG1655
    
    iECx6
    
    iEC1344_C Escherichia coli C
    
    iEC1356_Bl21DE3 Escherichia coli BL21(DE3)
    
    iEC1349_Crooks Escherichia coli ATCC 8739
    
    iEC1364_W Escherichia coli W
    
    iEC1372_W3110 Escherichia coli str. K-12 substr. W3110
    
    iEC1368_DH5a Escherichia coli DH5[alpha] (DH5alpha)
    
    Shigella ∙ Shigella flexneri
    
    Shigella flexneri 2a ∙ Shigella flexneri 2a str. 301
    
    iSF_1195 Shigella flexneri 2a str. 301
    
    Salmonella ∙ Salmonella enterica
    
    Salmonella enterica subsp. enterica ∙ Salmonella enterica subsp. enterica serovar Typhimurium ∙ Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
    
    STM_v1_0 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
    
    Klebsiella/Raoultella group ∙ Klebsiella ∙ Klebsiella pneumoniae complex ∙ Klebsiella pneumoniae
    
    Klebsiella pneumoniae subsp. pneumoniae ∙ Klebsiella pneumoniae subsp. pneumoniae MGH 78578
    
    iYL1228 Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (ATCC 700721; MGH 78578)
    
    iECx55
    
    iECNA114_1301 Escherichia coli NA114
    
    iEcE24377_1341 Escherichia coli O139:H28 str. E24377A
    
    iECO103_1326 Escherichia coli O103:H2 str. 12009
    
    iECO111_1330 Escherichia coli O111:H- str. 11128
    
    iECO26_1355 Escherichia coli O26:H11 str. 11368
    
    iECOK1_1307 Escherichia coli IHE3034
    
    iEcolC_1368 Escherichia coli ATCC 8739
    
    iECP_1309 Escherichia coli 536
    
    iECW_1372 Escherichia coli W
    
    iEKO11_1354 Escherichia coli KO11
    
    iETEC_1333 Escherichia coli ETEC H10407
    
    iG2583_1286 Escherichia coli O55:H7 str. CB9615
    
    iLF82_1304 Escherichia coli LF82
    
    iSBO_1134 Shigella boydii Sb227
    
    iSDY_1059 Shigella dysenteriae Sd197
    
    iSFV_1184 Shigella flexneri 5 str. 8401
    
    iECED1_1282 Escherichia coli ED1a
    
    ic_1306 Escherichia coli CFT073
    
    iE2348C_1286 Escherichia coli O127:H6 str. E2348/69
    
    iEcHS_1320 Escherichia coli HS
    
    iEC042_1314 Escherichia coli 042
    
    iEC55989_1330 Escherichia coli 55989
    
    iECIAI1_1343 Escherichia coli IAI1
    
    iECABU_c1320 Escherichia coli ABU 83972
    
    iECS88_1305 Escherichia coli S88
    
    iECs_1301 Escherichia coli O157:H7 str. Sakai
    
    iBWG_1329 Escherichia coli BW2952 (K-12)
    
    iECSE_1348 Escherichia coli SE11
    
    iECBD_1354 Escherichia coli 'BL21-Gold(DE3)pLysS AG'
    
    iB21_1397 Escherichia coli BL21(DE3)
    
    iECSF_1327 Escherichia coli SE15
    
    iNRG857_1313 Escherichia coli O83:H1 str. NRG 857C
    
    iECD_1391 Escherichia coli BL21(DE3)
    
    iEcSMS35_1347 Escherichia coli SMS-3-5
    
    iS_1188 Shigella flexneri 2a str. 2457T
    
    iECSP_1301 Escherichia coli O157:H7 str. TW14359
    
    iEcDH1_1363 Escherichia coli DH1
    
    iECUMN_1333 Escherichia coli UMN026
    
    iECDH1ME8569_1439 Escherichia coli DH1
    
    iECDH10B_1368 Escherichia coli str. K-12 substr. DH10B
    
    iSFxv_1172 Shigella flexneri 2002017
    
    iSSON_1240 Shigella sonnei Ss046
    
    iUMN146_1321 Escherichia coli UM146
    
    iUMNK88_1353 Escherichia coli UMNK88
    
    iUTI89_1310 Escherichia coli UTI89
    
    iWFL_1372 Escherichia coli W
    
    iECIAI39_1322 Escherichia coli IAI39
    
    iECH74115_1262 Escherichia coli O157:H7 str. EC4115
    
    iECB_1328 Escherichia coli B str. REL606
    
    iSbBS512_1146 Shigella boydii CDC 3083-94 (BS512; CDC 3083-94)
    
    iZ_1308 Escherichia coli O157:H7 str. EDL933
    
    Yersiniaceae
    
    Yersinia ∙ Yersinia pseudotuberculosis complex ∙ Yersinia pestis
    
    Yersinia pestis CO92
    
    iPC815 Yersinia pestis CO92
    
    Pseudomonadales ∙ Pseudomonadaceae
    
    Pseudomonas ∙ Pseudomonas putida group ∙ Pseudomonas putida
    
    Pseudomonas putida KT2440
    
    iJN746 Pseudomonas putida KT2440
    
    iJN1463 Pseudomonas putida KT2440
    
    Moraxellales ∙ Moraxellaceae
    
    Acinetobacter ∙ Acinetobacter calcoaceticus/baumannii complex ∙ Acinetobacter baumannii
    
    Acinetobacter baumannii AYE
    
    iCN718 Acinetobacter baumannii AYE
    
    Campylobacterota ∙ Epsilonproteobacteria
    
    Campylobacterales ∙ Helicobacteraceae
    
    Helicobacter ∙ Helicobacter pylori
    
    Helicobacter pylori 26695
    
    iIT341 Helicobacter pylori 26695
    
    Thermodesulfobacteriota ∙ Desulfuromonadia
    
    Geobacterales ∙ Geobacteraceae
    
    Geobacter ∙ Geobacter metallireducens
    
    Geobacter metallireducens GS-15
    
    iAF987 Geobacter metallireducens GS-15
  - Bacillati
    
    Bacillota
    
    Clostridia
    
    Eubacteriales ∙ Clostridiaceae
    
    Clostridium ∙ [Clostridium] innocuum
    
    iPKB_Clostridiaceae
    
    iPKB_GCF_042849295_1 [Clostridium] innocuum (k08-0096-A4)
    
    iPKB_GCF_964246095_1 [Clostridium] innocuum 2959
    
    iPKB_GCF_902652195_1 [Clostridium] innocuum
    
    iPKB_GCF_022693575_1 [Clostridium] innocuum (LK5-005)
    
    iPKB_GCF_009876425_1 [Clostridium] innocuum (BIOML-A2)
    
    iPKB_GCF_020709335_1 [Clostridium] innocuum (DFI.2.33)
    
    iPKB_GCF_964252575_1 [Clostridium] innocuum 2959
    
    iPKB_GCF_027695885_1 [Clostridium] innocuum (LG100-28)
    
    iPKB_GCF_964239715_1 [Clostridium] innocuum 2959
    
    iPKB_GCF_002814255_1 [Clostridium] innocuum (2959)
    
    iPKB_GCF_964252455_1 [Clostridium] innocuum 2959
    
    iPKB_GCF_003459885_1 [Clostridium] innocuum (AF18-35LB)
    
    iPKB_GCF_964243945_1 [Clostridium] innocuum 2959
    
    iPKB_GCF_009874205_1 [Clostridium] innocuum (BIOML-A4)
    
    iPKB_GCF_009874145_1 [Clostridium] innocuum (BIOML-A11)
    
    iPKB_GCF_964246375_1 [Clostridium] innocuum 2959
    
    iPKB_GCF_003149285_1 [Clostridium] innocuum (NLAE-zl-G197)
    
    iPKB_GCF_964240785_1 [Clostridium] innocuum 2959
    
    iPKB_GCF_964245125_1 [Clostridium] innocuum 2959
    
    iPKB_GCF_009696405_1 [Clostridium] innocuum (BSM-380-WT-2D)
    
    iPKB_GCF_022693475_1 [Clostridium] innocuum (MRL7493)
    
    iPKB_GCF_964252475_1 [Clostridium] innocuum 2959
    
    iPKB_GCF_964239495_1 [Clostridium] innocuum
    
    iPKB_GCF_964243965_1 [Clostridium] innocuum 2959
    
    iPKB_GCF_020709235_1 [Clostridium] innocuum (DFI.4.57)
    
    iPKB_GCF_900116735_1 [Clostridium] innocuum (NLAE-zl-G197)
    
    iPKB_GCF_002221705_2 [Clostridium] innocuum (I46)
    
    iPKB_GCF_964242455_1 [Clostridium] innocuum
    
    iPKB_GCF_041226065_1 [Clostridium] innocuum (5-285)
    
    iPKB_GCF_964248735_1 [Clostridium] innocuum 2959
    
    iPKB_GCF_020709465_1 [Clostridium] innocuum (DFI.5.67)
    
    iPKB_GCF_009874195_1 [Clostridium] innocuum (BIOML-A7)
    
    iPKB_GCF_964251365_1 [Clostridium] innocuum 2959
    
    iPKB_GCF_964251825_1 [Clostridium] innocuum 2959
    
    iPKB_GCF_019125695_1 [Clostridium] innocuum (MSK.5.23)
    
    iPKB_GCF_009876375_1 [Clostridium] innocuum (BIOML-A5)
    
    iPKB_GCF_012271835_1 [Clostridium] innocuum (LC-LUMC-CI-001)
    
    iPKB_GCF_051064475_1 [Clostridium] innocuum (332F)
    
    iPKB_GCF_009874155_1 [Clostridium] innocuum (BIOML-A6)
    
    iPKB_GCF_964242285_1 [Clostridium] innocuum 2959
    
    iPKB_GCF_015550705_1 [Clostridium] innocuum (1001285H_161024_B5)
    
    iPKB_GCF_022693435_1 [Clostridium] innocuum (MRL6604)
    
    iPKB_GCF_964250425_1 [Clostridium] innocuum 2959
    
    iPKB_GCF_022845735_1 [Clostridium] innocuum (CE91-St51)
    
    iPKB_GCF_964251955_1 [Clostridium] innocuum 2959
    
    iPKB_GCF_022693485_1 [Clostridium] innocuum (MRL6598)
    
    iPKB_GCF_964248195_1 [Clostridium] innocuum 2959
    
    iPKB_GCF_009874095_1 [Clostridium] innocuum (BIOML-A13)
    
    iPKB_GCF_039832195_1 [Clostridium] innocuum (AN406)
    
    iPKB_GCF_903181455_1 [Clostridium] innocuum
    
    iPKB_GCF_027691005_1 [Clostridium] innocuum (TF03-11)
    
    iPKB_GCF_022693565_1 [Clostridium] innocuum (LK3P-181)
    
    iPKB_GCF_900114575_1 [Clostridium] innocuum (NLAE-zl-C381)
    
    iPKB_GCF_964240515_1 [Clostridium] innocuum 2959
    
    iPKB_GCF_023008265_1 [Clostridium] innocuum (VE303-07)
    
    iPKB_GCF_964249425_1 [Clostridium] innocuum 2959
    
    iPKB_GCF_964249565_1 [Clostridium] innocuum 2959
    
    iPKB_GCF_020709535_1 [Clostridium] innocuum (DFI.2.56)
    
    iPKB_GCF_022693625_1 [Clostridium] innocuum (LK3P-180)
    
    iPKB_GCF_964250005_1 [Clostridium] innocuum 2959
    
    iPKB_GCF_020709455_1 [Clostridium] innocuum (DFI.4.59)
    
    iPKB_GCF_022693545_1 [Clostridium] innocuum (LK5-043)
    
    iPKB_GCF_020709385_1 [Clostridium] innocuum (DFI.2.55)
    
    iPKB_GCF_009876415_1 [Clostridium] innocuum (BIOML-A1)
    
    iPKB_GCF_009876385_1 [Clostridium] innocuum (BIOML-A8)
    
    iPKB_GCF_001406695_1 [Clostridium] innocuum (2789STDY5834853)
    
    iPKB_GCF_902374605_1 [Clostridium] innocuum
    
    iPKB_GCF_009876345_1 [Clostridium] innocuum (BIOML-A9)
    
    iPKB_GCF_042847175_1 [Clostridium] innocuum (f20)
    
    iPKB_GCF_018458805_1 [Clostridium] innocuum (ATCC 14501)
    
    iPKB_GCF_022693425_1 [Clostridium] innocuum (MRL7460)
    
    iPKB_GCF_019131515_1 [Clostridium] innocuum (MSK.13.34)
    
    iPKB_GCF_022132425_1 [Clostridium] innocuum (DFI.4.58)
    
    iPKB_GCF_964247825_1 [Clostridium] innocuum 2959
    
    iPKB_GCF_020709285_1 [Clostridium] innocuum (DFI.2.54)
    
    iPKB_GCF_964248465_1 [Clostridium] innocuum 2959
    
    iPKB_GCF_902166045_1 [Clostridium] innocuum (4928STDY7387914)
    
    iPKB_GCF_009874055_1 [Clostridium] innocuum (BIOML-A12)
    
    iPKB_GCF_964252155_1 [Clostridium] innocuum
    
    iPKB_GCF_012317185_1 [Clostridium] innocuum (ATCC 14501)
    
    iPKB_GCF_020709245_1 [Clostridium] innocuum (DFI.2.68)
    
    iPKB_GCF_964241105_1 [Clostridium] innocuum
    
    iPKB_GCF_964251295_1 [Clostridium] innocuum
    
    iPKB_GCF_964249795_1 [Clostridium] innocuum
    
    iPKB_GCF_020709315_1 [Clostridium] innocuum (DFI.2.25)
    
    iPKB_GCF_019130895_1 [Clostridium] innocuum (MSK.15.85)
    
    iPKB_GCF_964246075_1 [Clostridium] innocuum 2959
    
    iPKB_GCF_020709275_1 [Clostridium] innocuum (DFI.4.74)
    
    iPKB_GCF_902166105_1 [Clostridium] innocuum (4928STDY7387913)
    
    iPKB_GCF_051065075_1 [Clostridium] innocuum (258F)
    
    iPKB_GCF_040093915_1 [Clostridium] innocuum (CLA-AA-H251)
    
    iPKB_GCF_009874135_1 [Clostridium] innocuum (BIOML-A10)
    
    iPKB_GCF_964249895_1 [Clostridium] innocuum 2959
    
    iPKB_GCF_016697325_1 [Clostridium] innocuum (I46)
    
    iPKB_GCF_022693525_1 [Clostridium] innocuum (MRL5543)
    
    iPKB_GCF_039521305_1 [Clostridium] innocuum (JCM 1292)
    
    iPKB_GCF_027687515_1 [Clostridium] innocuum (AF07-33B)
    
    Peptostreptococcales ∙ Peptostreptococcaceae
    
    Clostridioides ∙ Clostridioides difficile
    
    Clostridioides difficile 630
    
    iCN900 Clostridioides difficile 630
    
    Bacilli
    
    Bacillales
    
    Staphylococcaceae
    
    Staphylococcus ∙ Staphylococcus aureus
    
    Staphylococcus aureus subsp. aureus N315
    
    iSB619 Staphylococcus aureus subsp. aureus N315
    
    Bacillaceae
    
    Bacillus ∙ Bacillus subtilis group ∙ Bacillus subtilis
    
    Bacillus subtilis subsp. subtilis ∙ Bacillus subtilis subsp. subtilis str. 168
    
    iYO844 Bacillus subtilis subsp. subtilis str. 168
    
    Lactobacillales ∙ Streptococcaceae
    
    Lactococcus ∙ Lactococcus cremoris
    
    Lactococcus cremoris subsp. cremoris ∙ Lactococcus cremoris subsp. cremoris MG1363
    
    iNF517 Lactococcus cremoris subsp. cremoris MG1363
    
    Cyanobacteriota/Melainabacteria group ∙ Cyanobacteriota ∙ Cyanophyceae
    
    Synechococcales
    
    Synechococcaceae
    
    Synechococcus ∙ Synechococcus elongatus
    
    Synechococcus elongatus PCC 7942 = FACHB-805
    
    iJB785 Synechococcus elongatus PCC 7942 = FACHB-805
    
    Merismopediaceae
    
    Synechocystis ∙ unclassified Synechocystis ∙ Synechocystis sp. PCC 6803
    
    iJN678 Synechocystis sp. PCC 6803
    
    iSynCJ816 Synechocystis sp. PCC 6803
    
    Actinomycetota ∙ Actinomycetes
    
    Mycobacteriales ∙ Mycobacteriaceae
    
    Mycobacterium ∙ Mycobacterium tuberculosis complex ∙ Mycobacterium tuberculosis
    
    Mycobacterium tuberculosis H37Rv
    
    iNJ661 Mycobacterium tuberculosis H37Rv
    
    iEK1008 Mycobacterium tuberculosis H37Rv
- Eukaryota
  - Sar
    
    Alveolata ∙ Apicomplexa ∙ Aconoidasida
    
    Haemosporida ∙ Plasmodiidae
    
    Plasmodium
    
    iAM_Px5
    
    iAM_Pf480 Plasmodium falciparum 3D7
    
    iAM_Pv461 Plasmodium vivax (Salvador I)
    
    iAM_Pb448 Plasmodium berghei ANKA
    
    iAM_Pc455 Plasmodium cynomolgi strain B
    
    iAM_Pk459 Plasmodium knowlesi strain H
    
    Stramenopiles ∙ Ochrophyta ∙ Bacillariophyta ∙ Bacillariophyceae
    
    Bacillariophycidae ∙ Naviculales ∙ Phaeodactylaceae
    
    Phaeodactylum ∙ Phaeodactylum tricornutum
    
    Phaeodactylum tricornutum CCAP 1055/1
    
    iLB1027_lipid Phaeodactylum tricornutum CCAP 1055/1
  - Opisthokonta
    
    Fungi ∙ Dikarya ∙ Ascomycota ∙ saccharomyceta ∙ Saccharomycotina ∙ Saccharomycetes
    
    Saccharomycetales ∙ Saccharomycetaceae
    
    Saccharomyces ∙ Saccharomyces cerevisiae
    
    Saccharomyces cerevisiae S288C
    
    iMM904 Saccharomyces cerevisiae S288C
    
    iND750 Saccharomyces cerevisiae S288C
    
    Metazoa ∙ Eumetazoa ∙ Bilateria ∙ Deuterostomia ∙ Chordata ∙ Craniata ∙ Vertebrata ∙ Gnathostomata ∙ Teleostomi ∙ Euteleostomi ∙ Sarcopterygii ∙ Dipnotetrapodomorpha ∙ Tetrapoda ∙ Amniota ∙ Mammalia
    
    Theria ∙ Eutheria ∙ Boreoeutheria ∙ Euarchontoglires ∙ Primates ∙ Haplorrhini ∙ Simiiformes ∙ Catarrhini ∙ Hominoidea ∙ Hominidae
    
    Homininae ∙ Homo ∙ Homo sapiens
    
    RECON1 Homo sapiens
    
    iAT_PLT_636 Homo sapiens
    
    iAB_RBC_283 Homo sapiens
- Archaea
  - Methanobacteriati ∙ Methanobacteriota ∙ Stenosarchaea group ∙ Methanomicrobia
    
    Methanosarcinales ∙ Methanosarcinaceae
    
    Methanosarcina ∙ Methanosarcina barkeri
    
    Methanosarcina barkeri str. Fusaro
    
    iAF692 Methanosarcina barkeri str. Fusaro