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 1-1
medoid: Serratia entomophila GCF 021462285 1
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AAI clade 1-2
medoid: Citrobacter freundii ATCC 8090 MTCC 1658 NBRC 12681 GCF 011064845 1
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AAI clade 1-2-1
medoid: Shigella boydii GCF 003572535 1
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AAI clade 1-2-2
medoid: Citrobacter sedlakii NBRC 105722 GCF 000759835 1
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AAI clade 1-2-3
medoid: Citrobacter freundii ATCC 8090 MTCC 1658 NBRC 12681 GCF 011064845 1
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AAI clade 1-2-3-1
medoid: Citrobacter arsenatis GCF 004353845 1
7 datasets: Citrobacter freundii ATCC 8090 MTCC 1658 NBRC 12681 GCF 011064845 1 (AAI: 98.32%), Citrobacter werkmanii NBRC 105721 GCF 000759755 1 (AAI: 97.55%), Citrobacter braakii GCF 002075345 1 (AAI: 98.71%), Citrobacter arsenatis GCF 004353845 1 (AAI: 100.0%), Citrobacter europaeus GCF 900079995 3 (AAI: 98.73%), Citrobacter meridianamericanus GCF 024023655 1 (AAI: 98.22%), and Citrobacter portucalensis GCF 002042885 1 (AAI: 98.44%)
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AAI clade 1-2-3-2
medoid: Citrobacter pasteurii GCF 019047765 1
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AAI clade 1-2-3-3
medoid: Enterobacter kobei GCF 018323985 1
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AAI clade 1-2-3-4
medoid: Citrobacter tructae GCF 004684345 1
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AAI clade 1-2-3-5
medoid: Citrobacter enshiensis GCF 029338175 1
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AAI clade 1-2-3-1
medoid: Citrobacter arsenatis GCF 004353845 1
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AAI clade 1-2-4
medoid: Kluyvera sichuanensis GCF 014218705 1
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AAI clade 1-2-5
medoid: Buttiauxella gaviniae ATCC 51604 GCF 001654835 1
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AAI clade 1-2-1
medoid: Shigella boydii GCF 003572535 1
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AAI clade 1-3
medoid: Enterobacter chuandaensis GCF 003594915 1
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AAI clade 1-4
medoid: Vibrio rotiferianus CAIM 577 LMG 21460 GCF 002741985 1
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AAI clade 1-5
medoid: Aeromonas veronii bv veronii GCF 001908535 1
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AAI clade 1-6
medoid: Pectobacterium polonicum GCF 005497185 1
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AAI clade 1-7
medoid: Photorhabdus caribbeanensis GCF 018448885 1
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AAI clade 1-8
medoid: Vibrio crassostreae GCF 001048535 1
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AAI clade 1-9
medoid: Yersinia alsatica GCF 902170305 1
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AAI clade 1-10
medoid: Pantoea astica asm GCA 002434205 1
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AAI clade 1-11
medoid: Dickeya fangzhongdai GCF 002812485 1
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AAI clade 1-12
medoid: Limnobaculum allomyrinae GCF 016649425 1
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AAI clade 1-13
medoid: Photobacterium alginatilyticum GCF 009910675 1
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AAI clade 1-14
medoid: Providencia hangzhouensis GCF 029193595 2
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AAI clade 1-15
medoid: Xenorhabdus thuongxuanensis GCF 001908095 1
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AAI clade 1-16
medoid: Grimontia indica GCF 000333895 2
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AAI clade 1-17
medoid: Rahnella variigena GCF 003602185 1
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AAI clade 1-18
medoid: Oceanimonas doudoroffii GCF 002242685 1
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AAI clade 1-19
medoid: Proteus alimentorum GCF 002607735 1
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AAI clade 1-1
medoid: Serratia entomophila GCF 021462285 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 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