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 13-1
medoid: Bacteroides luhongzhouii GCF 009193295 2
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AAI clade 13-2
medoid: Marinifilum breve GCF 003202155 1
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AAI clade 13-3
medoid: Flavobacterium proteolyticum GCF 015223105 1
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AAI clade 13-4
medoid: Flavivirga abyssicola GCF 030540775 2
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AAI clade 13-5
medoid: Flavobacterium resistens GCF 009674815 1
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AAI clade 13-6
medoid: Tenacibaculum singaporense GCF 003867015 1
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AAI clade 13-7
medoid: Parabacteroides merdae ATCC 43184 GCF 025151215 1
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AAI clade 13-8
medoid: Prevotella vespertina GCF 009728485 1
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AAI clade 13-9
medoid: Salegentibacter agarivorans GCF 900113135 1
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AAI clade 13-10
medoid: Alistipes provencensis GCF 900083545 1
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AAI clade 13-11
medoid: Muricauda lutisoli GCF 017313105 1
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AAI clade 13-12
medoid: Chryseobacterium cucumeris GCF 001593385 1
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AAI clade 13-13
medoid: Fulvivirga ulvae GCF 021389975 1
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AAI clade 13-14
medoid: Flavobacterium yafengii GCF 030010375 1
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AAI clade 13-15
medoid: Mucilaginibacter endophyticus GCF 003351025 1
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AAI clade 13-16
medoid: Pedobacter riviphilus GCF 014692875 1
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AAI clade 13-17
medoid: Pontibacter ramchanderi GCF 002846395 1
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AAI clade 13-18
medoid: Algoriphagus algorifonticola GCF 007655305 1
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AAI clade 13-19
medoid: Sphingobacterium puteale GCF 003627955 1
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AAI clade 13-20
medoid: Aquimarina megaterium XH134 GCF 000520975 1
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AAI clade 13-21
medoid: Aequorivita aquimaris GCF 001573155 1
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AAI clade 13-22
medoid: Spirosoma aureum GCF 011604685 1
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AAI clade 13-23
medoid: Maribacter forsetii DSM 18668 GCF 000744105 1
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AAI clade 13-24
medoid: Chitinophaga eiseniae GCF 900167135 1
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AAI clade 13-24-1
medoid: Chitinophaga eiseniae GCF 900167135 1
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AAI clade 13-24-1-1
medoid: Chitinophaga lutea GCF 003813775 1
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AAI clade 13-24-1-2
medoid: Chitinophaga horti GCF 022867795 2
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AAI clade 13-24-1-3
medoid: Chitinophaga ginsengisegetis GCF 900168065 1
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AAI clade 13-24-1-4
medoid: Chitinophaga varians GCF 014529945 1
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AAI clade 13-24-1-4-1
medoid: Chitinophaga dinghuensis GCF 003259435 1
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AAI clade 13-24-1-4-2
medoid: Chitinophaga oryzae GCF 012516375 2
2 datasets: Chitinophaga eiseniae GCF 900167135 1 (AAI: 95.99%) and Chitinophaga oryzae GCF 012516375 2 (AAI: 100.0%)
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AAI clade 13-24-1-4-3
medoid: Chitinophaga flava GCF 003308995 1
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AAI clade 13-24-1-4-4
medoid: Chitinophaga varians GCF 014529945 1
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AAI clade 13-24-1-4-5
medoid: Chitinophaga jiangningensis GCF 900142605 1
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AAI clade 13-24-1-4-6
medoid: Chitinophaga qingshengii GCF 014529935 1
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AAI clade 13-24-1-4-7
medoid: Chitinophaga solisilvae GCF 009928525 1
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AAI clade 13-24-1-4-8
medoid: Chitinophaga vietnamensis GCF 902167635 1
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AAI clade 13-24-1-4-1
medoid: Chitinophaga dinghuensis GCF 003259435 1
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AAI clade 13-24-1-5
medoid: Phaeodactylibacter luteus GCF 007993045 1
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AAI clade 13-24-1-6
medoid: Portibacter marinus GCF 021533195 1
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AAI clade 13-24-1-1
medoid: Chitinophaga lutea GCF 003813775 1
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AAI clade 13-24-2
medoid: Chitinophaga ginsengisoli GCF 003014595 1
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AAI clade 13-24-3
medoid: Taibaiella helva GCF 003545695 1
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AAI clade 13-24-1
medoid: Chitinophaga eiseniae GCF 900167135 1
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AAI clade 13-25
medoid: Longitalea arenae GCF 016924755 1
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AAI clade 13-26
medoid: Dyadobacter psychrophilus GCF 900167945 1
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AAI clade 13-27
medoid: Winogradskyella thalassocola GCF 900099995 1
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AAI clade 13-28
medoid: Hymenobacter glacieicola GCF 014640315 1
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AAI clade 13-29
medoid: Fodinibius halophilus GCF 011059105 1
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AAI clade 13-30
medoid: Hymenobacter rubidus GCF 016734815 1
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AAI clade 13-1
medoid: Bacteroides luhongzhouii GCF 009193295 2
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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