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 1-1
medoid: Brucella intermedia GCA 900454225 1
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AAI clade 1-2
medoid: GCA 009773055 1
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AAI clade 1-3
medoid: GCF 013035315 1
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AAI clade 1-4
medoid: Agrobacterium leguminum GCA 015704895 1
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AAI clade 1-5
medoid: Azospirillum tabaci GCA 014596085 1
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AAI clade 1-6
medoid: Bartonella kosoyi GCA 003606325 3
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AAI clade 1-7
medoid: GCA 000985875 1
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AAI clade 1-8
medoid: Rhodobaca bogoriensis DSM 18756 GCA 004366635 1
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AAI clade 1-9
medoid: GCF 002153605 1
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AAI clade 1-10
medoid: Aureimonas phyllosphaerae GCA 014196405 1
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AAI clade 1-11
medoid: Gluconobacter oxydans GCA 001581045 1
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AAI clade 1-12
medoid: Paracoccus fontiphilus GCA 017356265 1
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AAI clade 1-13
medoid: Phyllobacterium myrsinacearum GCA 004217385 1
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AAI clade 1-14
medoid: GCF 016817355 1
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AAI clade 1-15
medoid: GCF 000813965 1
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AAI clade 1-16
medoid: GCA 902624095 1
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AAI clade 1-17
medoid: GCF 001999245 1
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AAI clade 1-17-1
medoid: Rhodobium orientis GCA 016653375 1
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AAI clade 1-17-2
medoid: Afifella marina DSM 2698 GCA 900102695 1
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AAI clade 1-17-3
medoid: Rhodomicrobium vannielii ATCC 17100 GCA 016461745 1
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AAI clade 1-17-4
medoid: Chelatococcus asaccharovorans GCA 018398275 1
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AAI clade 1-17-5
medoid: Chthonobacter rhizosphaerae GCA 013839525 1
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AAI clade 1-17-6
medoid: Pleomorphomonas carboxyditropha GCA 002770725 1
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AAI clade 1-17-7
medoid: Pseudovibrio ascidiaceicola GCA 900114245 1
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AAI clade 1-17-8
medoid: GCF 001999245 1
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AAI clade 1-17-9
medoid: GCA 009026145 1
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AAI clade 1-17-10
medoid: Pannonibacter indicus GCA 001418225 1
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AAI clade 1-17-11
medoid: GCF 009789575 1
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AAI clade 1-17-12
medoid: Acuticoccus sediminis GCA 003258595 1
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AAI clade 1-17-13
medoid: GCF 000526315 1
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AAI clade 1-17-14
medoid: Cohaesibacter marisflavi GCA 900115225 1
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AAI clade 1-17-15
medoid: Stappia sediminis GCA 009826895 1
8 datasets: Hongsoonwoonella zoysiae GCA 013266695 1 (AAI: 82.58%), Stappia albiluteola GCA 014050225 1 (AAI: 64.39%), Breoghania corrubedonensis GCA 003053845 1 (AAI: 57.44%), Stappia sediminis GCA 009826895 1 (AAI: 100.0%), GCA 002746425 1 (AAI: 51.66%), GCA 016865015 1 (AAI: 53.46%), GCA 017642935 1 (AAI: 53.07%), and GCA 019192585 1 (AAI: 53.39%)
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AAI clade 1-17-16
medoid: Prosthecodimorpha staleyi GCA 018729455 1
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AAI clade 1-17-17
medoid: Roseibium polysiphoniae GCA 014842925 1
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AAI clade 1-17-18
medoid: Kaistia granuli DSM 23481 GCA 000380505 1
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AAI clade 1-17-19
medoid: GCA 001516065 1
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AAI clade 1-17-20
medoid: Hyphomicrobium zavarzinii ATCC 27496 GCA 000383415 1
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AAI clade 1-17-21
medoid: GCA 017307955 1
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AAI clade 1-17-22
medoid: Rhodoligotrophos defluvii GCA 005281615 1
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AAI clade 1-17-23
medoid: Tepidamorphus gemmatus GCA 004346195 1
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AAI clade 1-17-24
medoid: Methyloceanibacter caenitepidi GCA 000828475 1
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AAI clade 1-17-25
medoid: Stappia stellulata DSM 5886 GCA 000423705 1
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AAI clade 1-17-26
medoid: GCA 002298965 1
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AAI clade 1-17-27
medoid: GCA 003574785 1
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AAI clade 1-17-28
medoid: GCA 002694595 1
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AAI clade 1-17-29
medoid: GCA 016522385 1
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AAI clade 1-17-30
medoid: GCA 016764535 1
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AAI clade 1-17-31
medoid: GCF 000230975 2
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AAI clade 1-17-1
medoid: Rhodobium orientis GCA 016653375 1
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AAI clade 1-18
medoid: GCF 001511835 1
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AAI clade 1-19
medoid: GCF 000948415 1
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AAI clade 1-20
medoid: Yoonia rosea GCA 900156505 1
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AAI clade 1-21
medoid: Rhizobium binae GCA 017357225 1
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AAI clade 1-22
medoid: GCF 002007205 1
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AAI clade 1-23
medoid: GCA 017991675 1
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AAI clade 1-24
medoid: Belnapia moabensis DSM 16746 GCA 000745835 1
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AAI clade 1-25
medoid: GCF 014204545 1
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AAI clade 1-26
medoid: GCA 018222605 1
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AAI clade 1-27
medoid: Devosia salina GCA 019504385 1
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AAI clade 1-28
medoid: Sulfitobacter dubius GCA 900113435 1
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AAI clade 1-29
medoid: GCA 900472485 1
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AAI clade 1-30
medoid: GCF 001713475 1
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AAI clade 1-31
medoid: Reyranella soli GCA 007992495 1
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AAI clade 1-32
medoid: GCF 900093605 1
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AAI clade 1-33
medoid: GCA 015228975 1
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AAI clade 1-34
medoid: GCA 001464425 1
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AAI clade 1-35
medoid: GCA 902547925 1
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AAI clade 1-36
medoid: GCA 902543145 1
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AAI clade 1-37
medoid: GCA 017546885 1
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AAI clade 1-38
medoid: miga PS19A ZeeviD 2015 PNP Main 103 megahit bin 23
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AAI clade 1-39
medoid: GCA 903879805 1
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AAI clade 1-40
medoid: GCA 902526865 1
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AAI clade 1-41
medoid: GCA 902602135 1
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AAI clade 1-1
medoid: Brucella intermedia GCA 900454225 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 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