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 3-8
medoid: Brevibacillus formosus GCF 003013405 1
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AAI clade 3-8-1
medoid: Aneurinibacillus migulanus GCF 006539965 1
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AAI clade 3-8-2
medoid: Brevibacillus formosus GCF 003013405 1
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AAI clade 3-8-3
medoid: Thermoactinomyces daqus GCF 000763315 1
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AAI clade 3-8-4
medoid: Alicyclobacillus contaminans DSM 17975 GCF 000429525 1
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AAI clade 3-8-5
medoid: Alkaliphilus flagellatus GCF 018919215 1
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AAI clade 3-8-6
medoid: Alicyclobacillus acidoterrestris ATCC 49025 GCF 000444055 1
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AAI clade 3-8-7
medoid: Alicyclobacillus sacchari GCF 004366795 1
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AAI clade 3-8-8
medoid: Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446 GCF 000024285 1
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AAI clade 3-8-9
medoid: Brevibacillus borstelensis GCF 003710865 1
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AAI clade 3-8-10
medoid: Polycladomyces subterraneus GCF 030433435 1
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AAI clade 3-8-11
medoid: Effusibacillus lacus GCF 002335525 1
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AAI clade 3-8-12
medoid: Sulfoacidibacillus thermotolerans GCF 003144315 1
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AAI clade 3-8-13
medoid: Planifilum fulgidum GCF 900113175 1
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AAI clade 3-8-14
medoid: Kroppenstedtia eburnea GCF 013282215 1
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AAI clade 3-8-15
medoid: Natranaerobius thermophilus JW NM WN LF GCF 000020005 1
2 datasets: Natranaerobius thermophilus JW NM WN LF GCF 000020005 1 (AAI: 100.0%) and Natranaerobius trueperi GCF 002216005 1 (AAI: 57.18%)
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AAI clade 3-8-16
medoid: Peptoniphilus gorbachii GCF 016908115 1
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AAI clade 3-8-17
medoid: Alicyclobacillus ferrooxydans GCF 001399675 1
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AAI clade 3-8-18
medoid: Alicyclobacillus kakegawensis NBRC 103104 GCF 001552655 1
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AAI clade 3-8-19
medoid: Tepidibacillus fermentans GCF 004342885 1
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AAI clade 3-8-20
medoid: Allorhodopirellula heiligendammensis GCF 007860105 1
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AAI clade 3-8-21
medoid: Anaeromonas frigoriresistens GCF 016820655 1
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AAI clade 3-8-22
medoid: Armatimonas rosea GCF 014202505 1
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AAI clade 3-8-23
medoid: Baia soyae GCF 004341445 1
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AAI clade 3-8-24
medoid: Chrysiogenes arsenatis DSM 11915 GCF 000469585 1
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AAI clade 3-8-25
medoid: Geovibrio thiophilus GCF 004087915 1
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AAI clade 3-8-26
medoid: Desulfocicer vacuolatum DSM 3385 GCF 900176365 1
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AAI clade 3-8-27
medoid: Gimesia alba GCF 007744675 1
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AAI clade 3-8-28
medoid: Natroniella acetigena GCF 023227745 1
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AAI clade 3-8-29
medoid: Helcococcus sueciensis DSM 17243 GCF 000423145 1
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AAI clade 3-8-30
medoid: Humisphaera borealis GCF 015169395 1
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AAI clade 3-8-31
medoid: Kyrpidia spormannii GCF 002804065 1
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AAI clade 3-8-32
medoid: Marininema halotolerans GCF 900116235 1
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AAI clade 3-8-33
medoid: Occallatibacter riparius GCF 025264625 1
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AAI clade 3-8-34
medoid: Shimazuella kribbensis DSM 45090 GCF 000428065 1
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AAI clade 3-8-35
medoid: Tindallia californiensis GCF 900107405 1
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AAI clade 3-8-36
medoid: Tumebacillus amylolyticus GCF 016722965 1
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AAI clade 3-8-37
medoid: Urinicoccus massiliensis GCF 900120405 1
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AAI clade 3-8-1
medoid: Aneurinibacillus migulanus GCF 006539965 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