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 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 15-1
medoid: Rhodobacter kunshanensis GCF 011059185 1
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AAI clade 15-2
medoid: Salipiger pentaromativorans GCF 024721115 1
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AAI clade 15-2-1
medoid: Mameliella sediminis GCF 019218285 1
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AAI clade 15-2-2
medoid: Salipiger abyssi GCF 001975705 1
8 datasets: Salipiger profundus GCF 014637265 1 (AAI: 73.04%), Salipiger aestuarii GCF 003259905 1 (AAI: 69.83%), Salipiger abyssi GCF 001975705 1 (AAI: 100.0%), Salipiger bermudensis HTCC2601 GCF 000153725 1 (AAI: 73.22%), Salipiger mucosus DSM 16094 GCF 000442255 1 (AAI: 67.72%), Salipiger pallidus GCF 014643635 1 (AAI: 70.7%), Salipiger pentaromativorans GCF 024721115 1 (AAI: 78.18%), and Salipiger thiooxidans GCF 900102075 1 (AAI: 73.93%)
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AAI clade 15-2-3
medoid: Alloyangia pacifica GCF 900100725 1
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AAI clade 15-2-4
medoid: Marivita geojedonensis GCF 002115805 1
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AAI clade 15-2-5
medoid: Palleronia marisminoris GCF 900113405 1
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AAI clade 15-2-6
medoid: Pseudooceanicola onchidii GCF 004959925 1
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AAI clade 15-2-7
medoid: Roseivivax jejudonensis GCF 900172265 1
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AAI clade 15-2-8
medoid: Tropicibacter naphthalenivorans GCF 001458375 1
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AAI clade 15-2-9
medoid: Albimonas donghaensis GCF 900106695 1
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AAI clade 15-2-10
medoid: Primorskyibacter flagellatus GCF 900176485 1
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AAI clade 15-2-11
medoid: Psychromarinibacter halotolerans GCF 029168315 1
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AAI clade 15-2-12
medoid: Puniceibacterium confluentis GCF 007923445 1
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AAI clade 15-2-13
medoid: Rhodosalinus halophilus GCF 003298775 1
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AAI clade 15-2-14
medoid: Roseicyclus mahoneyensis GCF 003148775 1
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AAI clade 15-2-15
medoid: Roseivivax halotolerans GCF 900115815 1
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AAI clade 15-2-1
medoid: Mameliella sediminis GCF 019218285 1
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AAI clade 15-3
medoid: Paracoccus versutus GCF 003387045 1
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AAI clade 15-4
medoid: Ruegeria intermedia GCF 900129345 1
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AAI clade 15-5
medoid: Phaeobacter piscinae GCF 002407245 1
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AAI clade 15-6
medoid: Roseovarius marisflavi GCF 900142625 1
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AAI clade 15-7
medoid: Limimaricola variabilis GCF 014195545 1
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AAI clade 15-8
medoid: Thioclava marina GCF 002020135 1
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AAI clade 15-9
medoid: Litoreibacter halocynthiae GCF 004365635 1
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AAI clade 15-10
medoid: Paracoccus fontiphilus GCF 017356265 1
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AAI clade 15-11
medoid: Sulfitobacter dubius GCF 900113435 1
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AAI clade 15-1
medoid: Rhodobacter kunshanensis GCF 011059185 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