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 13-8-1
medoid: Prevotella intermedia ATCC 25611 DSM 20706 GCF 001953955 1
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AAI clade 13-8-2
medoid: Prevotella melaninogenica ATCC 25845 GCF 000144405 1
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AAI clade 13-8-3
medoid: Segatella copri GCF 026015395 1
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AAI clade 13-8-4
medoid: Hallella mizrahii GCF 009695775 1
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AAI clade 13-8-5
medoid: Hoylesella oralis ATCC 33269 GCF 000185145 2
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AAI clade 13-8-6
medoid: Hallella multisaccharivorax DSM 17128 GCF 000218235 1
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AAI clade 13-8-7
medoid: Hoylesella timonensis 4401737 DSM 22865 JCM 15640 GCF 000430565 1
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AAI clade 13-8-8
medoid: Hoylesella loescheii DSM 19665 JCM 12249 ATCC 15930 GCF 000378085 1
3 datasets: Hoylesella loescheii DSM 19665 JCM 12249 ATCC 15930 GCF 000378085 1 (AAI: 100.0%), Hoylesella shahii DSM 15611 JCM 12083 GCF 000613445 1 (AAI: 78.6%), and Hoylesella saccharolytica JCM 17484 GCF 000614205 1 (AAI: 67.72%)
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AAI clade 13-8-9
medoid: Hoylesella marshii DSM 16973 JCM 13450 GCF 000146675 1
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AAI clade 13-8-10
medoid: Prevotella bivia DSM 20514 GCF 000262545 1
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AAI clade 13-8-11
medoid: Prevotella corporis DSM 18810 JCM 8529 GCF 000430525 1
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AAI clade 13-8-12
medoid: Prevotella marseillensis GCF 900625065 1
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AAI clade 13-8-13
medoid: Prevotella micans DSM 21469 JCM 16134 GCF 000373705 1
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AAI clade 13-8-14
medoid: Prevotella veroralis DSM 19559 JCM 6290 GCF 000377625 1
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AAI clade 13-8-15
medoid: Segatella albensis DSM 11370 JCM 12258 GCF 000426565 1
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AAI clade 13-8-16
medoid: Segatella baroniae DSM 16972 JCM 13447 GCF 000426585 1
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AAI clade 13-8-17
medoid: Segatella oris DSM 18711 JCM 12252 GCF 000377685 1
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AAI clade 13-8-18
medoid: Prevotella herbatica GCF 017347605 1
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AAI clade 13-8-19
medoid: Prevotella communis GCF 022024115 1
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AAI clade 13-8-20
medoid: Candidatus Equicola faecalis GCA 018065185 1
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AAI clade 13-8-21
medoid: Candidatus Prevotella equi GCA 018065145 1
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AAI clade 13-8-22
medoid: Hallella colorans GCF 003096815 1
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AAI clade 13-8-23
medoid: Hallella faecis GCF 018789675 1
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AAI clade 13-8-24
medoid: Hoylesella enoeca JCM 12259 GCF 000613405 1
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AAI clade 13-8-25
medoid: Hoylesella nanceiensis DSM 19126 JCM 15639 GCF 000379965 1
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AAI clade 13-8-26
medoid: Leyella lascolaii GCF 900079775 1
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AAI clade 13-8-27
medoid: Leyella stercorea DSM 18206 GCF 000235885 1
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AAI clade 13-8-28
medoid: Palleniella muris GCF 004792655 1
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AAI clade 13-8-29
medoid: Prevotella koreensis GCF 003977605 1
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AAI clade 13-8-30
medoid: Prevotella lacticifex GCF 019973375 1
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AAI clade 13-8-31
medoid: Segatella bryantii GCF 019973295 1
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AAI clade 13-8-32
medoid: Segatella buccae ATCC 33574 GCF 000184945 1
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AAI clade 13-8-33
medoid: Segatella cerevisiae GCF 024054555 1
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AAI clade 13-8-34
medoid: Xylanibacter muris GCF 013166605 1
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AAI clade 13-8-35
medoid: Xylanibacter oryzae DSM 17970 GCF 000585355 1
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AAI clade 13-8-1
medoid: Prevotella intermedia ATCC 25611 DSM 20706 GCF 001953955 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 13-26
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