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 5-1
medoid: Lactobacillus gallinarum DSM 10532 JCM 2011 GCF 001434975 1
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AAI clade 5-2
medoid: Lactococcus petauri GCF 002154895 1
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AAI clade 5-3
medoid: Streptococcus chosunense GCF 003626515 1
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AAI clade 5-4
medoid: Leuconostoc gelidum subsp. aenigmaticum GCF 020089505 1
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AAI clade 5-5
medoid: Lactiplantibacillus plantarum subsp. plantarum ATCC 14917 JCM 1149 CGMCC 1 2437 GCF 001434175 1
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AAI clade 5-6
medoid: Lacticaseibacillus casei DSM 20011 JCM 1134 ATCC 393 GCF 000829055 1
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AAI clade 5-7
medoid: Enterococcus faecium GCF 900447735 1
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AAI clade 5-8
medoid: Enterococcus haemoperoxidus ATCC BAA 382 GCF 000407165 1
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AAI clade 5-9
medoid: Apilactobacillus waqarii GCF 019061205 1
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AAI clade 5-10
medoid: Limosilactobacillus balticus GCF 014145615 1
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AAI clade 5-11
medoid: Streptococcus vicugnae GCF 016461705 1
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AAI clade 5-12
medoid: Lactobacillus isalae GCF 947539375 1
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AAI clade 5-13
medoid: Trichococcus paludicola GCF 003052295 1
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AAI clade 5-14
medoid: Lentilactobacillus buchneri DSM 20057 GCF 001434735 1
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AAI clade 5-15
medoid: Weissella confusa GCF 001436895 1
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AAI clade 5-16
medoid: Aerococcus mictus GCF 003286595 3
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AAI clade 5-17
medoid: Companilactobacillus zhachilii GCF 003606365 2
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AAI clade 5-18
medoid: Enterococcus hulanensis GCF 005405485 1
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AAI clade 5-19
medoid: Liquorilactobacillus mali GCF 001437155 1
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AAI clade 5-19-1
medoid: Ligilactobacillus acidipiscis GCF 001436945 1
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AAI clade 5-19-2
medoid: Ligilactobacillus murinus DSM 20452 NBRC 14221 GCF 001436015 1
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AAI clade 5-19-3
medoid: Ligilactobacillus agilis DSM 20509 GCF 001436215 1
6 datasets: Ligilactobacillus salivarius DSM 20555 ATCC 11741 GCF 000159395 1 (AAI: 65.4%), Ligilactobacillus ceti DSM 22408 GCF 000423245 1 (AAI: 60.48%), Ligilactobacillus equi DSM 15833 JCM 10991 GCF 000615765 1 (AAI: 66.58%), Ligilactobacillus hayakitensis DSM 18933 JCM 14209 GCF 000615845 1 (AAI: 63.63%), Ligilactobacillus agilis DSM 20509 GCF 001436215 1 (AAI: 100.0%), and Ligilactobacillus ubinensis GCF 024160875 1 (AAI: 69.85%)
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AAI clade 5-19-4
medoid: Liquorilactobacillus mali GCF 001437155 1
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AAI clade 5-19-5
medoid: Dellaglioa algida DSM 15638 GCF 001434695 1
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AAI clade 5-19-6
medoid: Ligilactobacillus araffinosus DSM 20653 GCF 001435375 1
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AAI clade 5-19-7
medoid: Liquorilactobacillus nagelii DSM 13675 GCF 001434225 1
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AAI clade 5-19-8
medoid: Liquorilactobacillus satsumensis DSM 16230 JCM 12392 GCF 001312045 1
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AAI clade 5-19-9
medoid: Liquorilactobacillus aquaticus DSM 21051 GCF 001436755 1
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AAI clade 5-19-10
medoid: Liquorilactobacillus vini DSM 20605 GCF 000255495 1
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AAI clade 5-19-1
medoid: Ligilactobacillus acidipiscis GCF 001436945 1
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AAI clade 5-20
medoid: Fructobacillus tropaeoli GCF 001047135 2
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AAI clade 5-21
medoid: Lactococcus laudensis GCF 013449735 1
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AAI clade 5-22
medoid: Levilactobacillus mulengensis GCF 003946045 1
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AAI clade 5-23
medoid: Alkalibacterium putridalgicola GCF 007988845 1
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AAI clade 5-24
medoid: Secundilactobacillus silagincola GCF 002583405 1
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AAI clade 5-25
medoid: Leptospira selangorensis GCF 004769405 1
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AAI clade 5-1
medoid: Lactobacillus gallinarum DSM 10532 JCM 2011 GCF 001434975 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