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: Rahnella aceris GCF 011684115 1
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AAI clade 2
medoid: Sinorhizobium saheli GCF 001651875 1
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AAI clade 3
medoid: Oceanobacillus limi GCF 900111445 1
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AAI clade 4
medoid: Pseudomonas alcaligenes GCF 900455475 1
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AAI clade 5
medoid: Alkalibacterium pelagium GCF 007991315 1
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AAI clade 6
medoid: Stenotrophomonas nematodicola GCF 009467805 1
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AAI clade 7
medoid: Thermaerobacter marianensis DSM 12885 GCF 000184705 1
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AAI clade 8
medoid: Megamonas hypermegale DSM 1672 GCF 000423385 1
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AAI clade 9
medoid: Actinomyces gaoshouyii GCF 002072175 1
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AAI clade 9-1
medoid: Bifidobacterium cebidarum GCF 009193305 1
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AAI clade 9-1-1
medoid: Bifidobacterium felsineum GCF 002802915 1
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AAI clade 9-1-2
medoid: Bifidobacterium indicum GCA 036986915 1
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AAI clade 9-1-3
medoid: Bifidobacterium pseudocatenulatum DSM 20438 JCM 1200 LMG 10505 GCF 000771445 1
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AAI clade 9-1-4
medoid: Gardnerella pickettii GCF 029226345 1
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AAI clade 9-1-5
medoid: Bifidobacterium simiiventris GCF 019331715 1
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AAI clade 9-1-6
medoid: Bifidobacterium erythrocebi GCF 012932675 1
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AAI clade 9-1-7
medoid: Bifidobacterium apri GCF 009299485 1
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AAI clade 9-1-8
medoid: Bifidobacterium pseudolongum subsp. globosum DSM 20092 GCF 002706665 1
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AAI clade 9-1-9
medoid: Bifidobacterium pullorum DSM 20433 GCF 000771405 1
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AAI clade 9-1-10
medoid: Bifidobacterium xylocopae GCF 003315615 1
2 datasets: Bifidobacterium actinocoloniiforme DSM 22766 GCF 000741095 1 (AAI: 72.97%) and Bifidobacterium xylocopae GCF 003315615 1 (AAI: 100.0%)
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AAI clade 9-1-11
medoid: Bifidobacterium animalis subsp. animalis GCF 000741485 1
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AAI clade 9-1-12
medoid: Bifidobacterium italicum GCF 002286915 1
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AAI clade 9-1-13
medoid: Bifidobacterium gallicum DSM 20093 LMG 11596 GCF 000741205 1
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AAI clade 9-1-14
medoid: Bifidobacterium lemurum GCF 014898175 1
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AAI clade 9-1-15
medoid: Bifidobacterium magnum DSM 20222 GCF 000771365 1
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AAI clade 9-1-16
medoid: Bifidobacterium minimum DSM 20102 GCF 000771245 1
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AAI clade 9-1-17
medoid: Bifidobacterium psychraerophilum GCF 000741705 1
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AAI clade 9-1-18
medoid: Bifidobacterium tibiigranuli GCF 009371885 1
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AAI clade 9-1-19
medoid: Aeriscardovia aeriphila GCF 002259595 1
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AAI clade 9-1-20
medoid: Bifidobacterium mizhiense GCF 020884755 1
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AAI clade 9-1-21
medoid: Bifidobacterium avesanii GCF 009299475 1
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AAI clade 9-1-22
medoid: Bifidobacterium miconis GCF 019331735 1
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AAI clade 9-1-23
medoid: Bifidobacterium bohemicum DSM 22767 GCF 000741525 1
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AAI clade 9-1-24
medoid: Bifidobacterium bombi DSM 19703 GCF 000737845 1
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AAI clade 9-1-25
medoid: Bifidobacterium rousetti GCF 008698235 1
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AAI clade 9-1-26
medoid: Bifidobacterium commune GCF 014191315 1
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AAI clade 9-1-27
medoid: Bifidobacterium mongoliense DSM 21395 GCF 000741285 1
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AAI clade 9-1-28
medoid: Parascardovia denticolens DSM 10105 JCM 12538 GCF 000191785 1
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AAI clade 9-1-29
medoid: Pseudoscardovia suis GCF 002259715 1
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AAI clade 9-1-30
medoid: Scardovia inopinata GCF 900445765 1
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AAI clade 9-1-31
medoid: Alloscardovia theropitheci GCF 004332295 1
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AAI clade 9-1-32
medoid: Bifidobacterium aemilianum GCF 003315635 1
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AAI clade 9-1-33
medoid: Bifidobacterium stellenboschense GCF 000741785 1
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AAI clade 9-1-34
medoid: Bifidobacterium aquikefiri GCF 002259795 1
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AAI clade 9-1-35
medoid: Bifidobacterium callimiconis GCF 003952005 1
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AAI clade 9-1-36
medoid: Bifidobacterium callitrichidarum GCF 003129905 1
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AAI clade 9-1-37
medoid: Bifidobacterium primatium GCF 002802875 1
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AAI clade 9-1-38
medoid: Bifidobacterium margollesii GCF 002860355 1
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AAI clade 9-1-39
medoid: Bifidobacterium olomucense GCF 012932375 1
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AAI clade 9-1-40
medoid: Bombiscardovia apis GCF 033095945 1
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AAI clade 9-1-1
medoid: Bifidobacterium felsineum GCF 002802915 1
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AAI clade 9-2
medoid: Actinomyces naeslundii GCF 031296655 1
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AAI clade 9-3
medoid: Arcanobacterium bovis GCF 004331995 1
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AAI clade 9-4
medoid: Cellulosimicrobium cellulans GCF 006539945 1
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AAI clade 9-5
medoid: Olsenella timonensis GCF 900119915 1
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AAI clade 9-1
medoid: Bifidobacterium cebidarum GCF 009193305 1
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AAI clade 10
medoid: Micromonospora sagamiensis GCF 014680085 1
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AAI clade 11
medoid: Nonomuraea indica GCF 002850745 1
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AAI clade 12
medoid: Jiella avicenniae GCF 021390325 1
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AAI clade 13
medoid: Chitinophaga terrae ex Kim and Jung 2007 GCF 900107795 1
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AAI clade 14
medoid: Zeimonas arvi GCF 008039575 1
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AAI clade 15
medoid: Cognatiyoonia koreensis GCF 900109295 1
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AAI clade 16
medoid: Legionella beliardensis GCF 900452395 1
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AAI clade 17
medoid: Dorea hominis GCF 014287705 1
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AAI clade 18
medoid: Massilia putida GCF 001941825 1
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AAI clade 19
medoid: Phycicoccus avicenniae GCF 018139485 1
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AAI clade 20
medoid: Lelliottia steviae GCF 015209785 1
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AAI clade 21
medoid: Natrarchaeobaculum aegyptiacum GCF 002156705 1
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AAI clade 22
medoid: Aquifex aeolicus VF5 GCF 000008625 1
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AAI clade 23
medoid: Campylobacter showae GCF 004803815 1
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AAI clade 24
medoid: Mannheimia bovis GCF 014541205 1
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AAI clade 25
medoid: Solobacterium moorei DSM 22971 GCF 000425005 1
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AAI clade 26
medoid: Neptunicella marina GCF 014270035 1
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AAI clade 27
medoid: Sphingomonas sabuli GCF 014352855 1
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AAI clade 28
medoid: Luteolibacter marinus GCF 014904755 1
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AAI clade 29
medoid: Mycoplasmoides genitalium GCF 036689675 1
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AAI clade 30
medoid: Brevundimonas huaxiensis GCF 014218725 1
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AAI clade 31
medoid: Lysobacter spongiicola DSM 21749 GCF 900167055 1
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AAI clade 32
medoid: Glycomyces dulcitolivorans GCF 003265355 1
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AAI clade 33
medoid: Methylovulum miyakonense HT12 GCF 000384075 1
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AAI clade 34
medoid: Candidatus Fiminaster equi GCA 018064745 1