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 3-1
medoid: Cytobacillus firmus GCF 900445365 1
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AAI clade 3-2
medoid: Lysinibacillus irui GCF 028877475 1
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AAI clade 3-3
medoid: Bacillus dicomae GCF 006494425 1
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AAI clade 3-4
medoid: Staphylococcus petrasii GCF 004684865 1
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AAI clade 3-5
medoid: Virgibacillus ndiopensis GCF 900187325 1
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AAI clade 3-6
medoid: Listeria innocua GCF 024721565 1
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AAI clade 3-7
medoid: Paenibacillus zanthoxyli JH29 GCF 000520715 1
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AAI clade 3-7-1
medoid: Paenibacillus timonensis GCF 022427145 1
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AAI clade 3-7-2
medoid: Paenibacillus kribbensis GCF 002240415 1
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AAI clade 3-7-3
medoid: Paenibacillus jilunlii GCF 001546055 1
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AAI clade 3-7-4
medoid: Paenibacillus thiaminolyticus NBRC 15656 DSM 7262 GCF 004001005 1
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AAI clade 3-7-5
medoid: Cohnella xylanilytica GCF 014212175 1
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AAI clade 3-7-6
medoid: Desulfobacula phenolica GCF 900105645 1
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AAI clade 3-7-7
medoid: Paenibacillus brevis GCF 018919145 1
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AAI clade 3-7-8
medoid: Paenibacillus lutimineralis GCF 003991425 1
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AAI clade 3-7-9
medoid: Paenibacillus radicis ex Gao et al 2016 GCF 014641555 1
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AAI clade 3-7-10
medoid: Paenibacillus taichungensis GCF 013359905 1
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AAI clade 3-7-11
medoid: Paenibacillus sophorae GCF 018966525 1
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AAI clade 3-7-12
medoid: Paenibacillus montanisoli GCF 003268025 1
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AAI clade 3-7-13
medoid: Paenibacillus endophyticus GCF 014192395 1
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AAI clade 3-7-14
medoid: Paenibacillus antarcticus GCF 001637225 1
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AAI clade 3-7-15
medoid: Paenibacillus lautus NBRC 15380 GCF 004000945 1
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AAI clade 3-7-16
medoid: Paenibacillus catalpae GCF 900112695 1
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AAI clade 3-7-17
medoid: Paenibacillus bovis GCF 001421015 2
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AAI clade 3-7-18
medoid: Paenibacillus pasadenensis DSM 19293 GCF 000422485 1
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AAI clade 3-7-19
medoid: Paenibacillus yonginensis GCF 001685395 1
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AAI clade 3-7-20
medoid: Paenibacillus dendrobii GCF 009807035 1
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AAI clade 3-7-21
medoid: Paenibacillus rhizovicinus GCF 010365285 1
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AAI clade 3-7-22
medoid: Saccharibacillus deserti GCF 013185225 1
5 datasets: Saccharibacillus deserti GCF 013185225 1 (AAI: 100.0%), Saccharibacillus kuerlensis DSM 22868 GCF 000378145 1 (AAI: 78.09%), Saccharibacillus alkalitolerans GCF 011090185 1 (AAI: 79.22%), Saccharibacillus brassicae GCF 006542275 1 (AAI: 86.73%), and Saccharibacillus qingshengii GCF 013185195 1 (AAI: 96.53%)
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AAI clade 3-7-23
medoid: Saccharibacillus endophyticus GCF 013185185 1
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AAI clade 3-7-24
medoid: Sebaldella termitidis ATCC 33386 GCF 000024405 1
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AAI clade 3-7-25
medoid: Thermobacillus composti KWC4 GCF 000227705 2
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AAI clade 3-7-26
medoid: Xylanibacillus composti GCF 018403685 1
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AAI clade 3-7-27
medoid: Cohnella cholangitidis GCF 014107495 1
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AAI clade 3-7-28
medoid: Paenibacillus pinisoli GCF 003605435 1
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AAI clade 3-7-29
medoid: Adhaeretor mobilis GCF 007741515 1
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AAI clade 3-7-30
medoid: Aureliella helgolandensis GCF 007752135 1
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AAI clade 3-7-31
medoid: Cohnella candidum GCF 003713065 1
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AAI clade 3-7-32
medoid: Cohnella hashimotonis GCF 030014955 1
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AAI clade 3-7-33
medoid: Desulfoluna spongiiphila GCF 900101345 1
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AAI clade 3-7-34
medoid: Desulfonema ishimotonii GCF 003851005 1
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AAI clade 3-7-35
medoid: Insulibacter thermoxylanivorax GCF 015472005 1
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AAI clade 3-7-36
medoid: Longirhabdus pacifica GCF 004115085 1
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AAI clade 3-7-37
medoid: Paenibacillus abyssi GCF 014640295 1
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AAI clade 3-7-38
medoid: Paenibacillus arenosi GCF 014841135 1
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AAI clade 3-7-39
medoid: Paenibacillus auburnensis GCF 927798115 1
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AAI clade 3-7-40
medoid: Paenibacillus etheri GCF 001012825 1
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AAI clade 3-7-41
medoid: Paenibacillus alkaliterrae GCF 021532375 1
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AAI clade 3-7-42
medoid: Paenibacillus segetis GCF 014639155 1
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AAI clade 3-7-43
medoid: Paenibacillus borealis GCF 000758665 1
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AAI clade 3-7-44
medoid: Paenibacillus bouchesdurhonensis GCF 900155685 1
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AAI clade 3-7-45
medoid: Paenibacillus cellulosilyticus GCF 003182255 1
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AAI clade 3-7-46
medoid: Paenibacillus sambharensis GCF 003233845 1
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AAI clade 3-7-47
medoid: Paenibacillus gallinarum GCF 014836635 1
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AAI clade 3-7-48
medoid: Paenibacillus terrigena DSM 21567 GCF 000374845 1
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AAI clade 3-7-49
medoid: Paenibacillus spongiae GCF 024734895 1
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AAI clade 3-7-50
medoid: Paenibacillus methanolicus GCF 008124765 1
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AAI clade 3-7-51
medoid: Paenibacillus oenotherae GCF 019443105 1
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AAI clade 3-7-52
medoid: Paenibacillus senegalimassiliensis GCF 001486585 1
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AAI clade 3-7-53
medoid: Paenibacillus zeisoli GCF 003994465 1
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AAI clade 3-7-54
medoid: Paenibacillus turpanensis GCF 011421635 1
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AAI clade 3-7-55
medoid: Streptobacillus ratti GCF 001891165 1
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AAI clade 3-7-56
medoid: Terracidiphilus gabretensis GCF 001449115 1
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AAI clade 3-7-1
medoid: Paenibacillus timonensis GCF 022427145 1
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AAI clade 3-8
medoid: Brevibacillus formosus GCF 003013405 1
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AAI clade 3-9
medoid: Mesoplasma coleopterae GCF 002804245 1
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AAI clade 3-10
medoid: Halalkalibacter alkaliphilus GCF 023555415 1
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AAI clade 3-11
medoid: Mycoplasmopsis glycophila ATCC 35277 GCF 000687855 1
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AAI clade 3-12
medoid: Paenibacillus alginolyticus DSM 5050 NBRC 15375 GCF 000422905 1
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AAI clade 3-13
medoid: Leptospira paudalimensis GCF 026151345 1
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AAI clade 3-1
medoid: Cytobacillus firmus GCF 900445365 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