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 2-1
medoid: Ochrobactrum gambitense gb CP098020
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AAI clade 2-2
medoid: Roseibium algicola GCF 001999245 1
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AAI clade 2-3
medoid: Rhizobium anhuiense GCF 003985145 1
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AAI clade 2-4
medoid: Bartonella elizabethae F9251 ATCC 49927 GCF 000518165 1
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AAI clade 2-5
medoid: Bradyrhizobium huanghuaihaiense GCF 007830635 1
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AAI clade 2-6
medoid: Sinorhizobium chiapasense GCF 036488675 1
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AAI clade 2-6-1
medoid: Sinorhizobium meliloti GCF 006539625 1
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AAI clade 2-6-2
medoid: Sinorhizobium glycinis GCF 001651865 1
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AAI clade 2-6-3
medoid: Shinella granuli GCF 004341885 1
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AAI clade 2-6-4
medoid: Ensifer adhaerens GCF 013283195 1
5 datasets: Ensifer adhaerens GCF 013283195 1 (AAI: 100.0%), Ensifer canadensis GCF 016865175 1 (AAI: 93.82%), Ensifer adhaerens GCF 000697965 2 (AAI: 80.71%), Ensifer oleiphilus GCF 013371465 1 (AAI: 95.8%), and Ensifer sesbaniae GCF 013283665 1 (AAI: 79.46%)
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AAI clade 2-6-5
medoid: Hoeflea alexandrii GCF 024105735 1
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AAI clade 2-6-6
medoid: Hoeflea prorocentri GCF 026735315 1
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AAI clade 2-6-7
medoid: Martelella radicis GCF 014196625 1
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AAI clade 2-6-8
medoid: Sinorhizobium chiapasense GCF 036488675 1
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AAI clade 2-6-9
medoid: Rhizobium quercicola GCF 021168455 1
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AAI clade 2-6-10
medoid: Pararhizobium haloflavum GCF 002750855 1
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AAI clade 2-6-11
medoid: Hellea balneolensis DSM 19091 GCF 000428525 1
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AAI clade 2-6-12
medoid: Rhizobium rhizolycopersici GCF 013378445 1
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AAI clade 2-6-13
medoid: Pararhizobium polonicum GCF 001687365 1
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AAI clade 2-6-14
medoid: Pararhizobium mangrovi GCF 006516965 1
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AAI clade 2-6-15
medoid: Pseudohoeflea suaedae GCF 004354915 1
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AAI clade 2-6-16
medoid: Rhizobium setariae GCF 016722925 1
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AAI clade 2-6-17
medoid: Xaviernesmea oryzae GCF 900109605 1
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AAI clade 2-6-1
medoid: Sinorhizobium meliloti GCF 006539625 1
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AAI clade 2-7
medoid: Acetobacter cerevisiae DSM 14362 GCF 025996195 1
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AAI clade 2-8
medoid: Mesorhizobium japonicum MAFF 303099 GCF 000009625 1
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AAI clade 2-9
medoid: Methylobacterium radiotolerans GCF 007991055 1
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AAI clade 2-10
medoid: Microvirga lotononidis GCF 000262405 1
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AAI clade 2-11
medoid: Devosia salina GCF 019504385 1
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AAI clade 2-1
medoid: Ochrobactrum gambitense gb CP098020
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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 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