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 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 17-1
medoid: Blautia hominis GCF 002270465 1
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AAI clade 17-2
medoid: Clostridium scindens ATCC 35704 GCF 000154505 1
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AAI clade 17-3
medoid: Clostridium moniliforme GCF 017873235 1
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AAI clade 17-4
medoid: Romboutsia timonensis GCF 900106845 1
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AAI clade 17-5
medoid: Faecalibacterium duncaniae GCF 010509575 1
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AAI clade 17-6
medoid: Lawsonibacter hominis GCF 014287895 1
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AAI clade 17-7
medoid: Clostridium indicum GCF 003432035 1
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AAI clade 17-8
medoid: Faecalispora jeddahensis GCF 000577335 1
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AAI clade 17-8-1
medoid: Neglectibacter timonensis GCF 900048895 1
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AAI clade 17-8-2
medoid: Anaerotruncus massiliensis ex Liu et al 2021 GCF 003665055 1
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AAI clade 17-8-3
medoid: Massiliimalia timonensis GCF 900186585 1
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AAI clade 17-8-4
medoid: Ligaoa zhengdingensis GCF 014384885 1
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AAI clade 17-8-5
medoid: Hominimerdicola aceti GCF 025567495 1
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AAI clade 17-8-6
medoid: Neobittarella massiliensis GCF 014269355 1
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AAI clade 17-8-7
medoid: Pseudobacteroides cellulosolvens ATCC 35603 DSM 2933 GCF 000745845 1
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AAI clade 17-8-8
medoid: Caproiciproducens faecalis GCF 019448085 1
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AAI clade 17-8-9
medoid: Candidatus Colimorpha enterica GCA 018065475 1
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AAI clade 17-8-10
medoid: Candidatus Coliplasma equi GCA 018065705 1
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AAI clade 17-8-11
medoid: Candidatus Limimonas coprohippi GCA 018065925 1
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AAI clade 17-8-12
medoid: Ruminococcus intestinalis GCF 014288065 1
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AAI clade 17-8-13
medoid: Caproicibacterium amylolyticum GCF 014467055 1
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AAI clade 17-8-14
medoid: Faecalispora jeddahensis GCF 000577335 1
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AAI clade 17-8-15
medoid: Ructibacterium gallinarum GCF 014982785 1
4 datasets: Congzhengia minquanensis GCF 014384785 1 (AAI: 49.3%), Hominilimicola fabiformis GCF 020687385 1 (AAI: 48.27%), Monoglobus pectinilyticus GCF 002874775 1 (AAI: 58.22%), and Ructibacterium gallinarum GCF 014982785 1 (AAI: 100.0%)
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AAI clade 17-8-16
medoid: Ruminococcus champanellensis 18P13 JCM 17042 GCF 000210095 1
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AAI clade 17-8-17
medoid: Candidatus Improbicoccus devescovinae GCA 036245095 1
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AAI clade 17-8-1
medoid: Neglectibacter timonensis GCF 900048895 1
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AAI clade 17-1
medoid: Blautia hominis GCF 002270465 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