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 4-1
medoid: Acinetobacter courvalinii GCF 008802255 1
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AAI clade 4-2
medoid: Pseudomonas congelans GCF 900103225 1
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AAI clade 4-3
medoid: Pseudomonas monsensis GCF 014268495 2
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AAI clade 4-4
medoid: Pseudomonas nitroreducens GCF 012986245 1
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AAI clade 4-5
medoid: Pseudomonas azotoformans GCF 900624915 1
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AAI clade 4-6
medoid: Pseudomonas chengduensis GCF 900102635 1
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AAI clade 4-7
medoid: Acinetobacter bouvetii DSM 14964 CIP 107468 GCF 000373725 1
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AAI clade 4-8
medoid: Moraxella equi GCF 002027555 1
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AAI clade 4-9
medoid: Halomonas ventosae GCF 004363555 1
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AAI clade 4-9-1
medoid: Halomonas elongata DSM 2581 GCF 000196875 2
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AAI clade 4-9-2
medoid: Cobetia marina GCF 001720485 1
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AAI clade 4-9-3
medoid: Halomonas getboli GCF 023094245 1
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AAI clade 4-9-4
medoid: Halomonas heilongjiangensis GCF 003202165 1
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AAI clade 4-9-5
medoid: Aidingimonas halophila GCF 014651655 1
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AAI clade 4-9-6
medoid: Halomonas anticariensis FP35 DSM 16096 GCF 000409775 1
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AAI clade 4-9-7
medoid: Halomonas sulfidoxydans GCF 017868775 1
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AAI clade 4-9-8
medoid: Halomonas cupida GCF 007991155 1
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AAI clade 4-9-9
medoid: Halomonas alimentaria GCF 009902005 1
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AAI clade 4-9-10
medoid: Halomonas aerodenitrificans GCF 021404405 1
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AAI clade 4-9-11
medoid: Halomonas lutea DSM 23508 GCF 000378505 1
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AAI clade 4-9-12
medoid: Marinospirillum insulare DSM 21763 GCF 000686905 1
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AAI clade 4-9-13
medoid: Oceanospirillum sediminis GCF 014164585 1
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AAI clade 4-9-14
medoid: Allopseudospirillum japonicum GCF 900108915 1
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AAI clade 4-9-15
medoid: Chromohalobacter nigrandesensis GCF 023061285 1
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AAI clade 4-9-16
medoid: Halomonas denitrificans GCF 003056305 1
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AAI clade 4-9-17
medoid: Halomonas mongoliensis GCF 031451685 1
4 datasets: Halomonas alkalicola GCF 030704205 1 (AAI: 82.44%), Halomonas campaniensis GCF 014193375 1 (AAI: 79.24%), Halomonas mongoliensis GCF 031451685 1 (AAI: 100.0%), and Halomonas pacifica GCF 007989625 1 (AAI: 70.49%)
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AAI clade 4-9-18
medoid: Halomonas alkalisoli GCF 021412585 1
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AAI clade 4-9-19
medoid: Halomonas maura GCF 030409305 1
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AAI clade 4-9-20
medoid: Halomonas ventosae GCF 004363555 1
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AAI clade 4-9-21
medoid: Halomonas faecis GCF 010993975 1
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AAI clade 4-9-22
medoid: Halomonas korlensis GCF 900116705 1
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AAI clade 4-9-23
medoid: Halomonas salinarum GCF 012062845 1
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AAI clade 4-9-24
medoid: Halomonas qiaohouensis GCF 031451695 1
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AAI clade 4-9-25
medoid: Modicisalibacter coralii GCF 004117855 1
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AAI clade 4-9-26
medoid: Marinospirillum alkaliphilum DSM 21637 GCF 900119735 1
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AAI clade 4-9-27
medoid: Marinospirillum perlucidum GCF 003336805 1
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AAI clade 4-9-28
medoid: Terasakiispira papahanaumokuakeensis GCF 001709345 1
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AAI clade 4-9-1
medoid: Halomonas elongata DSM 2581 GCF 000196875 2
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AAI clade 4-10
medoid: Pseudomonas songnenensis GCF 003696315 1
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AAI clade 4-11
medoid: Pseudomonas plecoglossicida GCF 030160515 1
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AAI clade 4-12
medoid: Psychrobacter aquimaris GCF 016107525 1
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AAI clade 4-13
medoid: Alloalcanivorax xenomutans GCF 900217905 1
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AAI clade 4-14
medoid: Marinobacterium sediminicola GCF 900184155 1
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AAI clade 4-15
medoid: Salinicola lusitanus GCF 003206045 1
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AAI clade 4-16
medoid: Seongchinamella unica GCF 004354085 1
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AAI clade 4-17
medoid: Halomonas alkaliphila GCF 033842765 1
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AAI clade 4-18
medoid: Marinobacter flavimaris GCF 003363485 1
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AAI clade 4-19
medoid: Microbulbifer marinus GCF 900107725 1
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AAI clade 4-20
medoid: Acidithiobacillus ferrooxidans ATCC 23270 GCF 000021485 1
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AAI clade 4-21
medoid: Ectothiorhodospira shaposhnikovii GCF 022227765 1
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AAI clade 4-22
medoid: Thalassolituus alkanivorans GCF 020447205 1
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AAI clade 4-23
medoid: Electrothrix rattekaaiensis asm GCA 032595675 1
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AAI clade 4-24
medoid: Halopseudomonas gallaeciensis GCF 003444685 1
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AAI clade 4-25
medoid: Maridesulfovibrio salexigens DSM 2638 GCF 000023445 1
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AAI clade 4-26
medoid: Endozoicomonas gorgoniicola GCF 025562715 2
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AAI clade 4-27
medoid: Allochromatium humboldtianum GCF 013385175 1
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AAI clade 4-28
medoid: Marinomonas lutimaris GCF 019426345 1
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AAI clade 4-29
medoid: Thiothrix lacustris DSM 21227 GCF 000621325 1
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AAI clade 4-1
medoid: Acinetobacter courvalinii GCF 008802255 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