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 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 33-1
medoid: Methylococcus mesophilus GCF 026247885 1
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AAI clade 33-2
medoid: Methylogaea oryzae GCF 019669985 1
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AAI clade 33-3
medoid: Methylomicrobium agile GCF 000733855 1
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AAI clade 33-4
medoid: Methylomonas denitrificans GCF 000785705 2
8 datasets: Methylomonas denitrificans GCF 000785705 2 (AAI: 100.0%), Methylomonas koyamae GCF 019669905 1 (AAI: 71.1%), Methylomarinum vadi GCF 000733935 1 (AAI: 59.17%), Methylomonas albis GCF 014850955 1 (AAI: 84.04%), Methylomonas fluvii GCF 014850975 1 (AAI: 87.62%), Methylomonas montana GCF 030490285 1 (AAI: 78.78%), Methylomonas rapida GCF 024360925 2 (AAI: 67.07%), and Methylomonas rhizoryzae GCF 008632455 1 (AAI: 63.13%)
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AAI clade 33-5
medoid: Methylobacter tundripaludum SV96 GCF 000190755 2
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AAI clade 33-6
medoid: Cycloclasticus pugetii PS 1 GCF 000384415 1
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AAI clade 33-7
medoid: Methylocaldum marinum GCF 003584645 1
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AAI clade 33-8
medoid: Methylovulum psychrotolerans GCF 002923755 1
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AAI clade 33-9
medoid: Methylomarinovum tepidoasis GCF 030294985 1
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AAI clade 33-10
medoid: Methyloprofundus sedimenti GCF 002072955 1
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AAI clade 33-11
medoid: Methylotetracoccus oryzae GCF 006175985 1
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AAI clade 33-12
medoid: Thiorhodococcus drewsii AZ1 GCF 000224065 1
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AAI clade 33-1
medoid: Methylococcus mesophilus GCF 026247885 1
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AAI clade 34
medoid: Candidatus Fiminaster equi GCA 018064745 1