AAI-based medoid clustering

The AAI clusters provide a good overview of the above-species structure of the datasets and facilitate taxonomic classification.

  • AAI clade 1 medoid: Rahnella aceris GCF 011684115 1
  • AAI clade 2 medoid: Sinorhizobium saheli GCF 001651875 1
  • AAI clade 3 medoid: Oceanobacillus limi GCF 900111445 1
    • AAI clade 3-1 medoid: Cytobacillus firmus GCF 900445365 1
    • AAI clade 3-2 medoid: Lysinibacillus irui GCF 028877475 1
    • AAI clade 3-3 medoid: Bacillus dicomae GCF 006494425 1
      • AAI clade 3-3-1 medoid: Bacillus dicomae GCF 006494425 1
        • AAI clade 3-3-1-1 medoid: Bacillus mycoides GCF 031316615 1
        • AAI clade 3-3-1-2 medoid: Bacillus fungorum GCF 002746455 1
          5 datasets: Bacillus anthracis GCF 022221345 1 (AAI: 96.08%), Bacillus albus GCF 001884185 1 (AAI: 97.26%), Bacillus dicomae GCF 006494425 1 (AAI: 97.02%), Bacillus fungorum GCF 002746455 1 (AAI: 100.0%), and Bacillus sanguinis GCF 018332475 1 (AAI: 96.27%)
        • AAI clade 3-3-1-3 medoid: Bacillus cereus ATCC 14579 GCF 006094295 1
        • AAI clade 3-3-1-4 medoid: Bacillus clarus GCF 000746925 1
        • AAI clade 3-3-1-5 medoid: Bacillus gaemokensis GCF 000712615 1
        • AAI clade 3-3-1-6 medoid: Bacillus mobilis GCF 001884045 1
        • AAI clade 3-3-1-7 medoid: Bacillus nitratireducens GCF 001884135 1
        • AAI clade 3-3-1-8 medoid: Bacillus toyonensis BCT 7112 GCF 000496285 1
        • AAI clade 3-3-1-9 medoid: Priestia taiwanensis GCF 014638355 1
        • AAI clade 3-3-1-10 medoid: Bacillus arachidis GCF 017498775 1
        • AAI clade 3-3-1-11 medoid: Bacillus bingmayongensis GCF 000299035 1
        • AAI clade 3-3-1-12 medoid: Bacillus cytotoxicus NVH 391 98 GCF 000017425 1
        • AAI clade 3-3-1-13 medoid: Bacillus hominis GCF 018332515 1
        • AAI clade 3-3-1-14 medoid: Bacillus luti GCF 001884105 1
        • AAI clade 3-3-1-15 medoid: Bacillus manliponensis GCF 000712595 1
        • AAI clade 3-3-1-16 medoid: Bacillus paramycoides GCF 001884235 1
        • AAI clade 3-3-1-17 medoid: Bacillus pseudomycoides DSM 12442 GCF 000161455 1
        • AAI clade 3-3-1-18 medoid: Bacillus rhizoplanae GCF 917563915 1
        • AAI clade 3-3-1-19 medoid: Ectobacillus antri GCF 003852715 1
        • AAI clade 3-3-1-20 medoid: Ectobacillus panaciterrae DSM 19096 GCF 000430785 1
        • AAI clade 3-3-1-21 medoid: Ectobacillus ponti GCF 024294785 1
        • AAI clade 3-3-1-22 medoid: Exiguobacterium alkaliphilum 12 1 GCF 000714435 1
        • AAI clade 3-3-1-23 medoid: Tannockella kyphosi GCF 021054785 1
      • AAI clade 3-3-2 medoid: Acholeplasma granularum ATCC 19168 GCF 000526235 1
      • AAI clade 3-3-3 medoid: Anaerococcus ihuae GCF 928368155 1
      • AAI clade 3-3-4 medoid: Senegalia massiliensis GCF 900626135 1
      • AAI clade 3-3-5 medoid: Anaerococcus murdochii GCF 019957155 1
      • AAI clade 3-3-6 medoid: Gottfriedia acidiceleris GCF 002128425 1
      • AAI clade 3-3-7 medoid: Peptoniphilus asaccharolyticus DSM 20463 GCF 900176115 1
      • AAI clade 3-3-8 medoid: Anaerococcus marasmi GCF 900290195 1
      • AAI clade 3-3-9 medoid: Anaerococcus provencensis GCF 000312365 2
      • AAI clade 3-3-10 medoid: Paracholeplasma morum GCF 016907055 1
    • AAI clade 3-4 medoid: Staphylococcus petrasii GCF 004684865 1
    • AAI clade 3-5 medoid: Virgibacillus ndiopensis GCF 900187325 1
    • AAI clade 3-6 medoid: Listeria innocua GCF 024721565 1
    • AAI clade 3-7 medoid: Paenibacillus zanthoxyli JH29 GCF 000520715 1
    • AAI clade 3-8 medoid: Brevibacillus formosus GCF 003013405 1
    • AAI clade 3-9 medoid: Mesoplasma coleopterae GCF 002804245 1
    • AAI clade 3-10 medoid: Halalkalibacter alkaliphilus GCF 023555415 1
    • AAI clade 3-11 medoid: Mycoplasmopsis glycophila ATCC 35277 GCF 000687855 1
    • AAI clade 3-12 medoid: Paenibacillus alginolyticus DSM 5050 NBRC 15375 GCF 000422905 1
    • AAI clade 3-13 medoid: Leptospira paudalimensis GCF 026151345 1
  • AAI clade 4 medoid: Pseudomonas alcaligenes GCF 900455475 1
  • AAI clade 5 medoid: Alkalibacterium pelagium GCF 007991315 1
  • AAI clade 6 medoid: Stenotrophomonas nematodicola GCF 009467805 1
  • AAI clade 7 medoid: Thermaerobacter marianensis DSM 12885 GCF 000184705 1
  • AAI clade 8 medoid: Megamonas hypermegale DSM 1672 GCF 000423385 1
  • AAI clade 9 medoid: Actinomyces gaoshouyii GCF 002072175 1
  • AAI clade 10 medoid: Micromonospora sagamiensis GCF 014680085 1
  • AAI clade 11 medoid: Nonomuraea indica GCF 002850745 1
  • AAI clade 12 medoid: Jiella avicenniae GCF 021390325 1
  • AAI clade 13 medoid: Chitinophaga terrae ex Kim and Jung 2007 GCF 900107795 1
  • AAI clade 14 medoid: Zeimonas arvi GCF 008039575 1
  • AAI clade 15 medoid: Cognatiyoonia koreensis GCF 900109295 1
  • AAI clade 16 medoid: Legionella beliardensis GCF 900452395 1
  • AAI clade 17 medoid: Dorea hominis GCF 014287705 1
  • AAI clade 18 medoid: Massilia putida GCF 001941825 1
  • AAI clade 19 medoid: Phycicoccus avicenniae GCF 018139485 1
  • AAI clade 20 medoid: Lelliottia steviae GCF 015209785 1
  • AAI clade 21 medoid: Natrarchaeobaculum aegyptiacum GCF 002156705 1
  • AAI clade 22 medoid: Aquifex aeolicus VF5 GCF 000008625 1
  • AAI clade 23 medoid: Campylobacter showae GCF 004803815 1
  • AAI clade 24 medoid: Mannheimia bovis GCF 014541205 1
  • AAI clade 25 medoid: Solobacterium moorei DSM 22971 GCF 000425005 1
  • AAI clade 26 medoid: Neptunicella marina GCF 014270035 1
  • AAI clade 27 medoid: Sphingomonas sabuli GCF 014352855 1
  • AAI clade 28 medoid: Luteolibacter marinus GCF 014904755 1
  • AAI clade 29 medoid: Mycoplasmoides genitalium GCF 036689675 1
  • AAI clade 30 medoid: Brevundimonas huaxiensis GCF 014218725 1
  • AAI clade 31 medoid: Lysobacter spongiicola DSM 21749 GCF 900167055 1
  • AAI clade 32 medoid: Glycomyces dulcitolivorans GCF 003265355 1
  • AAI clade 33 medoid: Methylovulum miyakonense HT12 GCF 000384075 1
  • AAI clade 34 medoid: Candidatus Fiminaster equi GCA 018064745 1