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 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 18-1 medoid: Burkholderia cepacia GCF 900446175 1
    • AAI clade 18-2 medoid: Roseateles asaccharophilus GCF 004362405 1
      • AAI clade 18-2-1 medoid: Caldimonas thermodepolymerans GCF 003349825 1
      • AAI clade 18-2-2 medoid: Albitalea terrae GCF 003852895 1
      • AAI clade 18-2-3 medoid: Ideonella dechloratans GCF 008801845 1
      • AAI clade 18-2-4 medoid: Inhella proteolytica GCF 016093275 1
      • AAI clade 18-2-5 medoid: Roseateles saccharophilus GCF 004342485 1
      • AAI clade 18-2-6 medoid: Rubrivivax benzoatilyticus JA2 ATCC BAA 35 GCF 000190375 1
      • AAI clade 18-2-7 medoid: Sphaerotilus sulfidivorans GCF 013426975 1
      • AAI clade 18-2-8 medoid: Aquabacterium parvum GCF 001447195 1
      • AAI clade 18-2-9 medoid: Rubrivivax pictus GCF 005403045 1
      • AAI clade 18-2-10 medoid: Aquariibacter albus GCF 014145335 1
      • AAI clade 18-2-11 medoid: Azohydromonas australica DSM 1124 GCF 000430725 1
      • AAI clade 18-2-12 medoid: Azohydromonas sediminis GCF 003574675 1
      • AAI clade 18-2-13 medoid: Caldimonas brevitalea GCF 001017435 1
      • AAI clade 18-2-14 medoid: Ideonella alba GCF 018069845 1
        4 datasets: Ideonella alba GCF 018069845 1 (AAI: 100.0%), Ideonella aquatica GCF 018069755 1 (AAI: 92.54%), Ideonella livida GCF 010499455 1 (AAI: 66.66%), and Ideonella paludis GCF 018069865 1 (AAI: 68.13%)
      • AAI clade 18-2-15 medoid: Methylibium petroleiphilum PM1 GCF 000015725 1
      • AAI clade 18-2-16 medoid: Mitsuaria chitosanitabida ATCC BAA 476 NBRC 102408 GCF 001598255 1
      • AAI clade 18-2-17 medoid: Roseateles oligotrophus GCF 025717515 1
      • AAI clade 18-2-18 medoid: Rivibacter subsaxonicus GCF 004217215 1
      • AAI clade 18-2-19 medoid: Roseateles depolymerans GCF 003387155 1
      • AAI clade 18-2-20 medoid: Roseateles toxinivorans GCF 004362525 1
      • AAI clade 18-2-21 medoid: Rubrivivax albus GCF 004016515 1
      • AAI clade 18-2-22 medoid: Rubrivivax rivuli GCF 004016505 1
      • AAI clade 18-2-23 medoid: Schlegelella koreensis GCF 013366375 1
      • AAI clade 18-2-24 medoid: Scleromatobacter humisilvae GCF 023231945 1
      • AAI clade 18-2-25 medoid: Sphaerotilus mobilis GCF 004216565 1
    • AAI clade 18-3 medoid: Acidovorax delafieldii GCF 007993815 1
    • AAI clade 18-4 medoid: Morococcus cerebrosus GCF 000813705 1
    • AAI clade 18-5 medoid: Paraburkholderia caffeinilytica GCF 902859905 1
    • AAI clade 18-6 medoid: Ralstonia wenshanensis GCF 021173085 1
    • AAI clade 18-7 medoid: Chromobacterium piscinae GCF 021129175 1
    • AAI clade 18-8 medoid: Massilia puerhi GCF 009861485 1
    • AAI clade 18-9 medoid: Cupriavidus alkaliphilus GCF 900094595 1
    • AAI clade 18-10 medoid: Pandoraea sputorum GCF 000814845 2
    • AAI clade 18-11 medoid: Paraburkholderia acidiphila GCF 009789655 1
    • AAI clade 18-12 medoid: Caballeronia zhejiangensis GCF 000698575 1
    • AAI clade 18-13 medoid: Silvimonas iriomotensis GCF 014645535 1
    • AAI clade 18-14 medoid: Corallococcus coralloides DSM 2259 GCF 000255295 1
    • AAI clade 18-15 medoid: Methylovorus mays GCF 020531915 1
    • AAI clade 18-16 medoid: Polynucleobacter corsicus GCF 018688255 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