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 5-1
medoid: GCF 014451325 1
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AAI clade 5-2
medoid: Streptomyces durocortorensis GCA 016901035 1
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AAI clade 5-3
medoid: Streptomyces platensis GCA 002119195 1
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AAI clade 5-4
medoid: Streptomyces tricolor GCA 002155905 1
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AAI clade 5-5
medoid: Nocardia araoensis NBRC 100135 GCA 000308435 1
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AAI clade 5-6
medoid: Amycolatopsis decaplanina DSM 44594 GCA 000342005 1
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AAI clade 5-7
medoid: GCF 001836165 1
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AAI clade 5-8
medoid: GCF 900199205 1
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AAI clade 5-9
medoid: GCF 006715225 1
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AAI clade 5-10
medoid: GCF 900323885 1
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AAI clade 5-10-1
medoid: Microbispora sitophila GCA 014892245 1
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AAI clade 5-10-2
medoid: GCF 014203605 1
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AAI clade 5-10-3
medoid: GCF 013363995 1
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AAI clade 5-10-4
medoid: GCF 900323885 1
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AAI clade 5-10-4-1
medoid: Nonomuraea coxensis DSM 45129 GCA 000379885 1
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AAI clade 5-10-4-2
medoid: Nonomuraea deserti GCA 004348685 1
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AAI clade 5-10-4-3
medoid: Nonomuraea jabiensis GCA 014204795 1
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AAI clade 5-10-4-4
medoid: Nonomuraea antri GCA 013283785 1
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AAI clade 5-10-4-5
medoid: GCF 008086045 1
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AAI clade 5-10-4-6
medoid: Nonomuraea zeae GCA 005889725 1
4 datasets: Nonomuraea cypriaca GCA 015645445 1 (AAI: 79.75%), Nonomuraea solani GCA 900108335 1 (AAI: 80.98%), Nonomuraea spiralis GCA 014648435 1 (AAI: 79.59%), and Nonomuraea zeae GCA 005889725 1 (AAI: 100.0%)
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AAI clade 5-10-4-7
medoid: Nonomuraea typhae GCA 009760925 1
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AAI clade 5-10-4-8
medoid: Nonomuraea aridisoli GCA 003236395 1
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AAI clade 5-10-4-9
medoid: Nonomuraea soli GCA 013761175 1
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AAI clade 5-10-4-10
medoid: Nonomuraea africana GCA 014873535 1
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AAI clade 5-10-4-11
medoid: Nonomuraea pusilla GCA 900109355 1
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AAI clade 5-10-4-12
medoid: Nonomuraea basaltis GCA 005893125 1
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AAI clade 5-10-4-13
medoid: Thermoactinospora rubra GCA 002093975 1
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AAI clade 5-10-4-14
medoid: GCA 013362835 1
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AAI clade 5-10-4-15
medoid: GCA 903970315 1
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AAI clade 5-10-4-1
medoid: Nonomuraea coxensis DSM 45129 GCA 000379885 1
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AAI clade 5-10-5
medoid: Nonomuraea guangzhouensis GCA 019396345 1
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AAI clade 5-10-6
medoid: Planotetraspora phitsanulokensis GCA 016863295 1
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AAI clade 5-10-7
medoid: Sphaerisporangium krabiense GCA 016863355 1
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AAI clade 5-10-8
medoid: Streptosporangium roseum DSM 43021 GCA 000024865 1
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AAI clade 5-10-9
medoid: Thermopolyspora flexuosa GCA 014647775 1
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AAI clade 5-10-10
medoid: Acrocarpospora pleiomorpha GCA 009687885 1
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AAI clade 5-10-11
medoid: Spongiactinospora gelatinilytica GCA 003236385 1
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AAI clade 5-10-12
medoid: Herbidospora galbida GCA 005233835 1
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AAI clade 5-10-13
medoid: Microtetraspora fusca GCA 001570365 1
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AAI clade 5-10-14
medoid: GCA 003565155 1
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AAI clade 5-10-1
medoid: Microbispora sitophila GCA 014892245 1
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AAI clade 5-11
medoid: GCA 002529455 1
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AAI clade 5-12
medoid: Lentzea atacamensis GCA 003269295 1
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AAI clade 5-13
medoid: GCF 900143215 1
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AAI clade 5-14
medoid: GCF 008327685 1
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AAI clade 5-15
medoid: GCF 002979475 1
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AAI clade 5-16
medoid: asm GCA 000754525 1
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AAI clade 5-1
medoid: GCF 014451325 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