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 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 21-1
medoid: Haloarcula marismortui ATCC 43049 GCF 000011085 1
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AAI clade 21-2
medoid: Haloferax marisrubri GCF 001469875 2
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AAI clade 21-3
medoid: Halorubrum salipaludis GCF 002286985 1
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AAI clade 21-4
medoid: Halobacterium hubeiense GCF 001488575 1
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AAI clade 21-5
medoid: Methanohalophilus portucalensis FDF 1 GCF 003722115 1
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AAI clade 21-6
medoid: Natrinema marinum GCF 024296685 1
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AAI clade 21-7
medoid: Archaeoglobus fulgidus DSM 4304 GCF 000008665 1
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AAI clade 21-8
medoid: Pyrodictium delaneyi GCF 001412615 1
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AAI clade 21-9
medoid: Haladaptatus litoreus GCF 900156425 1
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AAI clade 21-10
medoid: Halorussus limi GCF 023238205 1
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AAI clade 21-11
medoid: Methanosarcina vacuolata Z 761 GCF 000969905 1
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AAI clade 21-12
medoid: Methanobacterium formicicum GCF 029848115 1
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AAI clade 21-13
medoid: Methanocaldococcus bathoardescens GCF 000739065 1
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AAI clade 21-14
medoid: Acidianus ambivalens GCF 009428885 1
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AAI clade 21-15
medoid: Thermococcus thermotolerans GCF 024707485 1
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AAI clade 21-16
medoid: Pyrobaculum aerophilum str. IM2 GCF 000007225 1
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AAI clade 21-17
medoid: Wolframiiraptor gerlachensis asm GCA 021323375 2
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AAI clade 21-18
medoid: Methanococcoides orientis GCF 021184045 1
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AAI clade 21-19
medoid: Halobellus limi GCF 004799685 1
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AAI clade 21-20
medoid: Haloglomus halophilum GCF 024298885 1
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AAI clade 21-21
medoid: Halococcus qingdaonensis GCF 024508235 1
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AAI clade 21-22
medoid: Haloprofundus halophilus GCF 003439925 1
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AAI clade 21-23
medoid: Haloplanus rubicundus GCF 003342675 1
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AAI clade 21-24
medoid: Halosimplex pelagicum GCF 013415905 1
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AAI clade 21-25
medoid: Methanobrevibacter thaueri GCF 003111625 1
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AAI clade 21-26
medoid: Methanoculleus sediminis GCF 001017125 1
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AAI clade 21-26-1
medoid: Methanoculleus chikugoensis GCF 019669965 1
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AAI clade 21-26-2
medoid: Methanocorpusculum labreanum Z GCF 000015765 1
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AAI clade 21-26-3
medoid: Methanocalculus chunghsingensis GCF 018132105 1
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AAI clade 21-26-4
medoid: Methanocorpusculum vombati GCF 026891935 1
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AAI clade 21-26-5
medoid: Methanofollis aquaemaris GCF 017357525 1
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AAI clade 21-26-6
medoid: Methanofollis liminatans DSM 4140 GCF 000275865 1
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AAI clade 21-26-7
medoid: Methanogenium organophilum GCF 026684035 1
4 datasets: Methanogenium cariaci JCM 10550 GCF 001315945 1 (AAI: 66.01%), Methanogenium marinum GCF 028912405 1 (AAI: 68.37%), Methanogenium organophilum GCF 026684035 1 (AAI: 100.0%), and Methanovulcanius yangii GCF 018687785 1 (AAI: 58.12%)
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AAI clade 21-26-8
medoid: Methanolacinia petrolearia DSM 11571 GCF 000147875 1
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AAI clade 21-26-9
medoid: Methanoregula formicica SMSP GCF 000327485 1
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AAI clade 21-26-10
medoid: Methanoplanus endosymbiosus GCF 024662215 1
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AAI clade 21-26-11
medoid: Methanospirillum hungatei JF 1 GCF 000013445 1
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AAI clade 21-26-1
medoid: Methanoculleus chikugoensis GCF 019669965 1
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AAI clade 21-27
medoid: Nitrosopumilus ureiphilus GCF 013407185 1
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AAI clade 21-28
medoid: Methanolobus vulcani GCF 900100715 1
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AAI clade 21-1
medoid: Haloarcula marismortui ATCC 43049 GCF 000011085 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