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 18-1
medoid: Burkholderia cepacia GCF 900446175 1
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AAI clade 18-2
medoid: Roseateles asaccharophilus GCF 004362405 1
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AAI clade 18-3
medoid: Acidovorax delafieldii GCF 007993815 1
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AAI clade 18-4
medoid: Morococcus cerebrosus GCF 000813705 1
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AAI clade 18-4-1
medoid: Neisseria lactamica ATCC 23970 GCF 000741965 1
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AAI clade 18-4-2
medoid: Alysiella crassa GCF 900445245 1
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AAI clade 18-4-3
medoid: Morococcus cerebrosus GCF 000813705 1
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AAI clade 18-4-4
medoid: Neisseria zoodegmatis GCF 002108575 1
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AAI clade 18-4-5
medoid: Eikenella corrodens GCF 900187105 1
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AAI clade 18-4-6
medoid: Kingella oralis GCF 014054985 1
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AAI clade 18-4-7
medoid: Bergeriella denitrificans GCF 900453875 1
3 datasets: Neisseria animalis GCF 008806995 1 (AAI: 82.52%), Bergeriella denitrificans GCF 900453875 1 (AAI: 100.0%), and Neisseria chenwenguii GCF 002216145 1 (AAI: 72.68%)
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AAI clade 18-4-8
medoid: Neisseria subflava GCF 031190635 1
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AAI clade 18-4-9
medoid: Conchiformibius kuhniae GCA 022871025 1
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AAI clade 18-4-10
medoid: Kingella potus GCF 022870985 1
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AAI clade 18-4-11
medoid: Uruburuella testudinis GCF 022870865 1
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AAI clade 18-4-12
medoid: Neisseria wadsworthii 9715 GCF 000227765 1
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AAI clade 18-4-13
medoid: Neisseria yangbaofengii GCF 011038745 1
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AAI clade 18-4-14
medoid: Snodgrassella gandavensis GCF 914768025 1
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AAI clade 18-4-15
medoid: Vitreoscilla massiliensis GCF 001457815 1
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AAI clade 18-4-16
medoid: Eikenella glucosivorans GCF 016025525 2
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AAI clade 18-4-17
medoid: Neisseria montereyensis GCF 024834045 1
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AAI clade 18-4-18
medoid: Neisseria shayeganii 871 GCF 000226875 1
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AAI clade 18-4-19
medoid: Paralysiella testudinis GCF 016894345 1
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AAI clade 18-4-20
medoid: Stenoxybacter acetivorans DSM 19021 GCF 000745895 1
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AAI clade 18-4-21
medoid: Kingella pumchi GCF 022288825 1
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AAI clade 18-4-1
medoid: Neisseria lactamica ATCC 23970 GCF 000741965 1
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AAI clade 18-5
medoid: Paraburkholderia caffeinilytica GCF 902859905 1
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AAI clade 18-6
medoid: Ralstonia wenshanensis GCF 021173085 1
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AAI clade 18-7
medoid: Chromobacterium piscinae GCF 021129175 1
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AAI clade 18-8
medoid: Massilia puerhi GCF 009861485 1
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AAI clade 18-9
medoid: Cupriavidus alkaliphilus GCF 900094595 1
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AAI clade 18-10
medoid: Pandoraea sputorum GCF 000814845 2
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AAI clade 18-11
medoid: Paraburkholderia acidiphila GCF 009789655 1
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AAI clade 18-12
medoid: Caballeronia zhejiangensis GCF 000698575 1
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AAI clade 18-13
medoid: Silvimonas iriomotensis GCF 014645535 1
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AAI clade 18-14
medoid: Corallococcus coralloides DSM 2259 GCF 000255295 1
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AAI clade 18-15
medoid: Methylovorus mays GCF 020531915 1
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AAI clade 18-16
medoid: Polynucleobacter corsicus GCF 018688255 1
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AAI clade 18-1
medoid: Burkholderia cepacia GCF 900446175 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