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 3-9
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 3-13-1
medoid: Leptospira kirschneri serovar Cynopteri str. 3522 CT GCF 000243695 2
8 datasets: Leptospira interrogans GCF 900156205 1 (AAI: 92.33%), Leptospira alexanderi serovar Manhao 3 str. L 60 GCF 000243815 2 (AAI: 76.21%), Leptospira borgpetersenii serovar Javanica GCF 003046425 1 (AAI: 76.09%), Leptospira ellisii GCF 002811955 2 (AAI: 75.67%), Leptospira kirschneri serovar Cynopteri str. 3522 CT GCF 000243695 2 (AAI: 100.0%), Leptospira mayottensis 200901116 GCF 000306675 2 (AAI: 76.06%), Leptospira noguchii serovar Panama str. CZ214 GCF 000306255 2 (AAI: 87.87%), and Leptospira santarosai serovar Shermani str. LT 821 GCF 000313175 2 (AAI: 76.71%)
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AAI clade 3-13-2
medoid: Leptospira ainlahdjerensis GCF 016919175 1
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AAI clade 3-13-3
medoid: Leptospira abararensis GCF 016918735 1
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AAI clade 3-13-4
medoid: Leptospira paudalimensis GCF 026151345 1
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AAI clade 3-13-5
medoid: Leptospira fluminis GCF 004771275 1
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AAI clade 3-13-6
medoid: Turneriella parva DSM 21527 GCF 000266885 1
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AAI clade 3-13-1
medoid: Leptospira kirschneri serovar Cynopteri str. 3522 CT GCF 000243695 2
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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