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 13-25
medoid: Longitalea arenae GCF 016924755 1
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AAI clade 13-25-1
medoid: Niabella agricola GCF 021538615 1
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AAI clade 13-25-2
medoid: Longitalea arenae GCF 016924755 1
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AAI clade 13-25-2-1
medoid: Filimonas zeae GCF 014641615 1
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AAI clade 13-25-2-2
medoid: Hydrotalea sandarakina GCF 003254115 1
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AAI clade 13-25-2-3
medoid: Niastella yeongjuensis GCF 002077935 1
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AAI clade 13-25-2-4
medoid: Pseudoflavitalea rhizosphaerae GCF 003991355 1
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AAI clade 13-25-2-5
medoid: Paraflavitalea soli GCF 003555545 1
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AAI clade 13-25-2-6
medoid: Arachidicoccus terrestris GCF 020042345 1
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AAI clade 13-25-2-7
medoid: Segetibacter aerophilus GCF 007991655 1
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AAI clade 13-25-2-8
medoid: Dinghuibacter silviterrae GCF 004366355 1
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AAI clade 13-25-2-9
medoid: Ferruginibacter albus GCF 020042285 1
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AAI clade 13-25-2-10
medoid: Flavihumibacter profundi GCF 020076305 1
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AAI clade 13-25-2-11
medoid: Flavisolibacter ginsenosidimutans GCF 007970805 1
4 datasets: Flavisolibacter ginsengisoli DSM 18119 GCF 900129295 1 (AAI: 63.6%), Flavisolibacter ginsenosidimutans GCF 007970805 1 (AAI: 100.0%), Flavisolibacter nicotianae GCF 003628535 1 (AAI: 67.51%), and Paraflavisolibacter caeni GCF 025628885 1 (AAI: 61.21%)
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AAI clade 13-25-2-12
medoid: Hanamia caeni GCF 003721595 1
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AAI clade 13-25-2-13
medoid: Haliscomenobacter hydrossis DSM 1100 GCF 000212735 1
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AAI clade 13-25-2-14
medoid: Sediminibacterium goheungense GCF 004361915 1
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AAI clade 13-25-2-15
medoid: Lacibacter cauensis GCF 007830055 1
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AAI clade 13-25-2-16
medoid: Panacibacter ginsenosidivorans GCF 007971225 1
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AAI clade 13-25-2-17
medoid: Longitalea arenae GCF 016924755 1
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AAI clade 13-25-2-18
medoid: Membranihabitans marinus GCF 021729155 1
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AAI clade 13-25-2-19
medoid: Pinibacter aurantiacus GCF 019130065 1
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AAI clade 13-25-2-20
medoid: Rhizosphaericola mali GCF 004337365 2
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AAI clade 13-25-2-21
medoid: Pollutibacter soli GCF 029269725 1
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AAI clade 13-25-2-1
medoid: Filimonas zeae GCF 014641615 1
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AAI clade 13-25-1
medoid: Niabella agricola GCF 021538615 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