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 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 11-1
medoid: Streptomyces tanashiensis GCF 014648895 1
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AAI clade 11-2
medoid: Kribbella sindirgiensis GCF 004331435 1
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AAI clade 11-3
medoid: Corynebacterium lehmanniae GCF 027570055 1
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AAI clade 11-4
medoid: Streptomyces sabulosicollis GCF 016103465 1
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AAI clade 11-5
medoid: Streptomyces tricolor GCF 002155905 1
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AAI clade 11-6
medoid: Nocardiopsis dassonvillei GCF 900638215 1
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AAI clade 11-7
medoid: Nonomuraea jabiensis GCF 014204795 1
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AAI clade 11-7-1
medoid: Nonomuraea jabiensis GCF 014204795 1
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AAI clade 11-7-2
medoid: Microbispora siamensis GCF 016863095 1
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AAI clade 11-7-2-1
medoid: Microbispora siamensis GCF 016863095 1
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AAI clade 11-7-2-2
medoid: Egicoccus halophilus GCF 004300825 1
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AAI clade 11-7-2-3
medoid: Fibrobacter succinogenes subsp. succinogenes S85 GCF 000024665 1
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AAI clade 11-7-2-4
medoid: Planotetraspora phitsanulokensis GCF 016863295 1
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AAI clade 11-7-2-5
medoid: Slackia exigua ATCC 700122 GCF 000162875 1
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AAI clade 11-7-2-6
medoid: Sphaerisporangium krabiense GCF 014200435 1
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AAI clade 11-7-2-7
medoid: Acidithrix ferrooxidans GCF 000949295 1
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AAI clade 11-7-2-8
medoid: Acrocarpospora pleiomorpha GCF 009687885 1
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AAI clade 11-7-2-9
medoid: Herbidospora galbida GCF 005233835 1
7 datasets: Herbidospora cretacea GCF 001570605 1 (AAI: 86.24%), Herbidospora daliensis GCF 001570585 1 (AAI: 94.21%), Herbidospora galbida GCF 005233835 1 (AAI: 100.0%), Herbidospora mongoliensis GCF 001570545 1 (AAI: 82.18%), Herbidospora sakaeratensis GCF 001570525 1 (AAI: 95.07%), Herbidospora solisilvae GCF 009901565 1 (AAI: 94.96%), and Herbidospora yilanensis GCF 001570565 1 (AAI: 94.5%)
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AAI clade 11-7-2-10
medoid: Microtetraspora fusca GCF 001570365 1
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AAI clade 11-7-2-1
medoid: Microbispora siamensis GCF 016863095 1
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AAI clade 11-7-1
medoid: Nonomuraea jabiensis GCF 014204795 1
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AAI clade 11-8
medoid: Nocardioides pinisoli GCF 024199985 1
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AAI clade 11-9
medoid: Actinomadura citrea GCF 013409045 1
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AAI clade 11-1
medoid: Streptomyces tanashiensis GCF 014648895 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