AAI-based medoid clustering
The AAI clusters provide a good overview of the above-species structure of the datasets and facilitate taxonomic classification.
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AAI clade 1
medoid: Brucella daejeonensis GCA 014199265 1
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AAI clade 2
medoid: GCA 017448355 1
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AAI clade 3
medoid: GCA 017467885 1
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AAI clade 4
medoid: Pedobacter duraquae GCA 004362245 1
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AAI clade 5
medoid: Streptomyces angustmyceticus GCA 002154415 1
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AAI clade 6
medoid: Pseudomonas migulae GCA 024169545 1
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AAI clade 7
medoid: miga SS18A Bin 41 contigs
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AAI clade 8
medoid: Mucilaginibacter ginkgonis GCA 009754905 2
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AAI clade 9
medoid: GCA 900755995 1
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AAI clade 10
medoid: GCF 013113835 1
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AAI clade 10-1
medoid: Pectobacterium polonicum GCA 005497185 1
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AAI clade 10-2
medoid: Serratia liquefaciens ATCC 27592 GCA 000422085 1
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AAI clade 10-3
medoid: Enterobacter oligotrophicus GCA 009176645 1
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AAI clade 10-3-1
medoid: Citrobacter farmeri GCA 019048065 1
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AAI clade 10-3-2
medoid: Klebsiella pneumoniae subsp. pneumoniae GCA 000788015 1
7 datasets: Klebsiella pneumoniae subsp. pneumoniae GCA 000788015 1 (AAI: 100.0%), Klebsiella quasipneumoniae GCA 020099175 1 (AAI: 98.64%), Klebsiella variicola GCA 000828055 2 (AAI: 97.79%), Klebsiella aerogenes GCA 019048125 1 (AAI: 92.94%), Pluralibacter gergoviae ATCC 33028 NBRC 105706 GCA 001598855 1 (AAI: 81.67%), GCA 019237635 1 (AAI: 83.87%), and miga PS19A VogtmannE 2016 MMRS86168210ST 27 0 0 bin 16 (AAI: 84.35%)
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AAI clade 10-3-3
medoid: Shigella boydii GCA 003572535 1
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AAI clade 10-3-4
medoid: GCF 001022965 1
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AAI clade 10-3-5
medoid: Cronobacter sakazakii NBRC 102416 GCA 000684935 1
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AAI clade 10-3-6
medoid: Citrobacter freundii ATCC 8090 MTCC 1658 NBRC 12681 GCA 000759735 1
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AAI clade 10-3-7
medoid: Klebsiella michiganensis GCA 002925905 1
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AAI clade 10-3-8
medoid: GCA 002360945 1
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AAI clade 10-3-9
medoid: Lelliottia nimipressuralis GCA 004115925 1
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AAI clade 10-3-10
medoid: Raoultella planticola GCA 004345285 1
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AAI clade 10-3-11
medoid: Shimwellia blattae GCA 900636035 1
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AAI clade 10-3-12
medoid: Trabulsiella guamensis ATCC 49490 GCA 000734965 1
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AAI clade 10-3-13
medoid: Atlantibacter subterranea GCA 027853245 1
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AAI clade 10-3-14
medoid: Buttiauxella gaviniae ATCC 51604 GCA 001654835 1
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AAI clade 10-3-15
medoid: GCF 000277545 1
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AAI clade 10-3-16
medoid: Kluyvera sichuanensis GCA 014218705 1
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AAI clade 10-3-17
medoid: Kosakonia sacchari GCA 900100995 1
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AAI clade 10-3-18
medoid: GCF 002918705 1
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AAI clade 10-3-19
medoid: GCA 000302695 1
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AAI clade 10-3-20
medoid: Scandinavium goeteborgense GCA 003935895 2
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AAI clade 10-3-21
medoid: Pseudocitrobacter vendiensis GCA 943590815 1
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AAI clade 10-3-22
medoid: GCA 900112785 1
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AAI clade 10-3-23
medoid: Dryocola boscaweniae GCA 025215095 1
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AAI clade 10-3-24
medoid: Mangrovibacter phragmitis GCA 001655675 1
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AAI clade 10-3-25
medoid: Superficieibacter electus GCA 002915575 1
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AAI clade 10-3-26
medoid: GCF 018323985 1
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AAI clade 10-3-1
medoid: Citrobacter farmeri GCA 019048065 1
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AAI clade 10-4
medoid: Vibrio rotiferianus CAIM 577 LMG 21460 GCA 002741985 1
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AAI clade 10-5
medoid: GCF 000217915 1
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AAI clade 10-6
medoid: Aeromonas veronii bv veronii GCA 018359905 1
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AAI clade 10-7
medoid: Pseudoalteromonas espejiana DSM 9414 GCA 002221525 1
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AAI clade 10-8
medoid: GCF 000210895 1
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AAI clade 10-9
medoid: Xenorhabdus griffiniae GCA 028598495 1
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AAI clade 10-10
medoid: GCF 001557875 1
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AAI clade 10-11
medoid: Yersinia alsatica GCA 902170305 1
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AAI clade 10-12
medoid: Photobacterium gaetbulicola Gung47 GCA 000940995 1
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AAI clade 10-13
medoid: GCA 002434205 1
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AAI clade 10-14
medoid: Rahnella variigena GCA 003602185 1
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AAI clade 10-15
medoid: Proteus alimentorum GCA 002607735 1
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AAI clade 10-16
medoid: Rheinheimera pacifica GCA 900108485 1
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AAI clade 10-17
medoid: Gilliamella bombicola GCA 900094945 1
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AAI clade 10-18
medoid: Succinivibrio dextrinosolvens DSM 3072 GCA 900167015 1
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AAI clade 10-19
medoid: GCF 005237295 1
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AAI clade 10-1
medoid: Pectobacterium polonicum GCA 005497185 1
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AAI clade 11
medoid: Secundilactobacillus odoratitofui DSM 19909 JCM 15043 GCA 001434895 1
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AAI clade 12
medoid: GCA 016840965 1
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AAI clade 13
medoid: GCA 017622235 1
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AAI clade 14
medoid: GCA 904390925 1
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AAI clade 15
medoid: GCA 002375985 1
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AAI clade 16
medoid: GCA 003963015 1
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AAI clade 17
medoid: GCA 001771585 1
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AAI clade 18
medoid: GCF 018398895 1
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AAI clade 19
medoid: GCA 001295775 1
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AAI clade 20
medoid: Qipengyuania aquimaris GCA 009827445 1
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AAI clade 21
medoid: GCF 009363535 1
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AAI clade 22
medoid: GCA 904374795 1
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AAI clade 23
medoid: GCA 903955385 1
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AAI clade 24
medoid: GCA 903887975 1
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AAI clade 25
medoid: GCA 902602655 1
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AAI clade 26
medoid: GCA 905235755 1
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AAI clade 27
medoid: Anaerovorax odorimutans DSM 5092 GCA 000426305 1
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AAI clade 28
medoid: GCA 903909555 1
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AAI clade 29
medoid: Marinomonas aquimarina GCA 900089755 1
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AAI clade 30
medoid: GCA 015061955 1
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AAI clade 31
medoid: GCA 000421065 1
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AAI clade 32
medoid: GCA 002438845 1
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AAI clade 33
medoid: GCA 003602665 1
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AAI clade 34
medoid: GCA 910585295 1
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AAI clade 35
medoid: Nocardioides iriomotensis GCA 004168035 1
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AAI clade 36
medoid: GCA 017608235 1
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AAI clade 37
medoid: GCF 004332155 1
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AAI clade 38
medoid: GCA 009712635 1
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AAI clade 39
medoid: GCA 903926605 1
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AAI clade 40
medoid: GCA 017645955 1
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AAI clade 41
medoid: GCA 016793015 1
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AAI clade 42
medoid: GCA 900538305 1
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AAI clade 43
medoid: GCA 001002765 1
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AAI clade 44
medoid: GCA 902559935 1
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AAI clade 45
medoid: GCA 011371455 1
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AAI clade 46
medoid: GCA 000435515 1
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AAI clade 47
medoid: Anaerostipes butyraticus GCA 016586355 1
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AAI clade 48
medoid: GCF 002835935 1
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AAI clade 49
medoid: miga PS19A RaymondF 2016 P20E90 bin 24
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AAI clade 50
medoid: GCA 002338255 1
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AAI clade 51
medoid: Haloprofundus salinisoli GCA 020097815 1
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AAI clade 52
medoid: GCA 900167925 1
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AAI clade 53
medoid: GCA 900550065 1
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AAI clade 54
medoid: GCA 002314915 1
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AAI clade 55
medoid: Rhizorhabdus dicambivorans GCA 002355275 1
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AAI clade 56
medoid: GCA 005882335 1
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AAI clade 57
medoid: GCA 011065225 1
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AAI clade 58
medoid: GCA 016781775 1
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AAI clade 59
medoid: GCA 002362595 1
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AAI clade 60
medoid: GCA 016214555 1
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AAI clade 61
medoid: GCF 014764505 1
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AAI clade 62
medoid: GCA 902623215 1
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AAI clade 63
medoid: GCA 003514205 1
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AAI clade 64
medoid: GCF 009707955 1
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AAI clade 65
medoid: GCF 000348745 1
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AAI clade 66
medoid: GCA 900772425 1
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AAI clade 67
medoid: GCF 003590645 1
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AAI clade 68
medoid: GCF 902506105 1
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AAI clade 69
medoid: GCF 013407275 1
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AAI clade 70
medoid: GCA 015494795 1
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AAI clade 71
medoid: GCA 016709995 1
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AAI clade 72
medoid: GCA 002493965 1
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AAI clade 73
medoid: GCA 009469665 1
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AAI clade 74
medoid: GCA 001799635 1
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AAI clade 75
medoid: GCA 016650235 1
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AAI clade 76
medoid: Ochrovirga pacifica GCA 000220525 2
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AAI clade 77
medoid: GCA 009903855 1
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AAI clade 78
medoid: GCA 019204045 1
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AAI clade 79
medoid: GCA 902783375 1
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AAI clade 80
medoid: GCF 000350105 1
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AAI clade 81
medoid: GCA 903901345 1
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AAI clade 82
medoid: GCA 015075425 1
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AAI clade 83
medoid: GCA 001508835 1
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AAI clade 84
medoid: GCA 017746715 1
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AAI clade 85
medoid: Nocardioides plantarum GCA 006346395 1
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AAI clade 86
medoid: GCA 017438285 1
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AAI clade 87
medoid: GCA 002712945 1
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AAI clade 88
medoid: GCF 002214625 1
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AAI clade 89
medoid: GCA 902773215 1
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AAI clade 90
medoid: GCA 002723385 1
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AAI clade 91
medoid: GCA 019113455 1
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AAI clade 92
medoid: GCA 016286935 1
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AAI clade 93
medoid: GCA 003566775 1