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 2-5-1
medoid: Bradyrhizobium ottawaense GCF 002278135 3
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AAI clade 2-5-2
medoid: Bradyrhizobium mercantei GCF 001982635 1
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AAI clade 2-5-3
medoid: Rhodoplanes tepidamans GCF 028550555 1
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AAI clade 2-5-4
medoid: Afipia birgiae 34632 GCF 000308295 2
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AAI clade 2-5-5
medoid: Bradyrhizobium forestalis GCF 002795245 1
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AAI clade 2-5-6
medoid: Rhodopseudomonas palustris GCF 003547145 1
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AAI clade 2-5-7
medoid: Bradyrhizobium icense GCF 001693385 1
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AAI clade 2-5-7-1
medoid: Bradyrhizobium murdochi GCF 000472965 1
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AAI clade 2-5-7-2
medoid: Bradyrhizobium jicamae GCF 001440395 1
3 datasets: Bradyrhizobium jicamae GCF 001440395 1 (AAI: 100.0%), Bradyrhizobium lablabi GCF 001440475 1 (AAI: 94.28%), and Bradyrhizobium paxllaeri GCF 001693515 2 (AAI: 93.88%)
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AAI clade 2-5-7-3
medoid: Bradyrhizobium roseus GCF 030413175 1
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AAI clade 2-5-7-4
medoid: Bradyrhizobium sediminis GCF 018736085 1
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AAI clade 2-5-7-5
medoid: Nitrobacter hamburgensis X14 GCF 000013885 1
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AAI clade 2-5-7-6
medoid: Nitrobacter vulgaris GCF 031453995 1
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AAI clade 2-5-7-7
medoid: Nitrobacter winogradskyi Nb 255 GCF 000012725 1
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AAI clade 2-5-7-8
medoid: Rhodopseudomonas boonkerdii GCF 021184025 1
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AAI clade 2-5-7-9
medoid: Rhodopseudomonas rhenobacensis GCF 014203125 1
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AAI clade 2-5-7-10
medoid: Tardiphaga robiniae GCF 013359755 1
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AAI clade 2-5-7-1
medoid: Bradyrhizobium murdochi GCF 000472965 1
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AAI clade 2-5-1
medoid: Bradyrhizobium ottawaense GCF 002278135 3
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AAI clade 2-6
medoid: Sinorhizobium chiapasense GCF 036488675 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