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 10-1
medoid: Mycolicibacterium senegalense GCF 031458155 1
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AAI clade 10-2
medoid: Mycobacterium parascrofulaceum ATCC BAA 614 GCF 000164135 1
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AAI clade 10-3
medoid: Rhodococcus wratislaviensis GCF 900455735 1
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AAI clade 10-4
medoid: Actinoplanes pyxinae GCF 026626335 1
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AAI clade 10-5
medoid: Corynebacterium tuberculostearicum GCF 013408445 1
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AAI clade 10-6
medoid: Micromonospora solifontis GCF 003725545 1
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AAI clade 10-6-1
medoid: Micromonospora vinacea GCF 015751785 1
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AAI clade 10-6-2
medoid: Catellatospora paridis GCF 009720365 1
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AAI clade 10-6-3
medoid: Micromonospora solifontis GCF 003725545 1
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AAI clade 10-6-3-1
medoid: Micromonospora solifontis GCF 003725545 1
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AAI clade 10-6-3-1-1
medoid: Micromonospora coxensis GCF 900090295 1
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AAI clade 10-6-3-1-2
medoid: Micromonospora zingiberis GCF 004331455 1
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AAI clade 10-6-3-1-3
medoid: Dactylosporangium siamense GCF 016862795 1
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AAI clade 10-6-3-1-4
medoid: Dactylosporangium fulvum GCF 025137375 1
4 datasets: Dactylosporangium matsuzakiense GCF 025264725 1 (AAI: 72.3%), Dactylosporangium fulvum GCF 025137375 1 (AAI: 100.0%), Dactylosporangium roseum GCF 025264685 1 (AAI: 87.72%), and Dactylosporangium sucinum GCF 014647515 1 (AAI: 78.32%)
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AAI clade 10-6-3-1-5
medoid: Micromonospora aurantiaca ATCC 27029 GCF 000145235 1
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AAI clade 10-6-3-1-6
medoid: Micromonospora fulviviridis GCF 014648395 1
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AAI clade 10-6-3-1-7
medoid: Micromonospora antibiotica GCF 017599305 1
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AAI clade 10-6-3-1-8
medoid: Micromonospora echinospora GCF 002266845 1
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AAI clade 10-6-3-1-9
medoid: Micromonospora andamanensis GCF 016863495 1
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AAI clade 10-6-3-1-10
medoid: Actinocatenispora sera GCF 000720965 1
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AAI clade 10-6-3-1-11
medoid: Asanoa hainanensis GCF 900188485 1
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AAI clade 10-6-3-1-12
medoid: Ferrimicrobium acidiphilum DSM 19497 GCF 000745905 1
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AAI clade 10-6-3-1-13
medoid: Longispora fulva GCF 015751905 1
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AAI clade 10-6-3-1-14
medoid: Micromonospora citrea GCF 900090315 1
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AAI clade 10-6-3-1-15
medoid: Phytomonospora endophytica GCF 014202425 1
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AAI clade 10-6-3-1-16
medoid: Planosporangium mesophilum GCF 011947235 1
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AAI clade 10-6-3-1-17
medoid: Acidimicrobium ferrooxidans DSM 10331 GCF 000023265 1
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AAI clade 10-6-3-1-18
medoid: Actinocatenispora rupis GCF 016861975 1
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AAI clade 10-6-3-1-19
medoid: Fodinicola acaciae GCF 010993745 1
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AAI clade 10-6-3-1-20
medoid: Longispora albida DSM 44784 GCF 000379825 1
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AAI clade 10-6-3-1-21
medoid: Micromonospora avicenniae GCF 900156065 1
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AAI clade 10-6-3-1-22
medoid: Micromonospora eburnea GCF 900090225 1
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AAI clade 10-6-3-1-23
medoid: Micromonospora kangleipakensis GCF 004217615 1
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AAI clade 10-6-3-1-24
medoid: Micromonospora mirobrigensis GCF 900091555 1
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AAI clade 10-6-3-1-25
medoid: Polymorphospora rubra GCF 018324255 1
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AAI clade 10-6-3-1-26
medoid: Miltoncostaea oceani GCF 018141545 1
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AAI clade 10-6-3-1-27
medoid: Natronosporangium hydrolyticum GCF 016925615 1
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AAI clade 10-6-3-1-28
medoid: Phytohabitans suffuscus GCF 011764565 1
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AAI clade 10-6-3-1-29
medoid: Pilimelia terevasa GCF 014647915 1
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AAI clade 10-6-3-1-30
medoid: Plantactinospora alkalitolerans GCF 015690345 1
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AAI clade 10-6-3-1-31
medoid: Plantactinospora mayteni GCF 016862935 1
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AAI clade 10-6-3-1-32
medoid: Rhabdothermincola sediminis GCF 014805525 1
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AAI clade 10-6-3-1-33
medoid: Rugosimonospora africana GCF 016862975 1
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AAI clade 10-6-3-1-34
medoid: Stackebrandtia endophytica GCF 006716355 1
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AAI clade 10-6-3-1-35
medoid: Stackebrandtia nassauensis DSM 44728 GCF 000024545 1
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AAI clade 10-6-3-1-36
medoid: Virgisporangium aliadipatigenens GCF 016863615 1
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AAI clade 10-6-3-1-37
medoid: Virgisporangium ochraceum GCF 016863655 1
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AAI clade 10-6-3-1-1
medoid: Micromonospora coxensis GCF 900090295 1
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AAI clade 10-6-3-2
medoid: Salinispora fenicalii GCF 000514815 1
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AAI clade 10-6-3-3
medoid: Catenuloplanes niger GCF 031458255 1
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AAI clade 10-6-3-1
medoid: Micromonospora solifontis GCF 003725545 1
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AAI clade 10-6-1
medoid: Micromonospora vinacea GCF 015751785 1
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AAI clade 10-7
medoid: Amycolatopsis decaplanina DSM 44594 GCF 000342005 1
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AAI clade 10-8
medoid: Gordonia alkanivorans NBRC 16433 GCF 000225505 1
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AAI clade 10-9
medoid: Nocardia araoensis NBRC 100135 GCF 000308435 1
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AAI clade 10-10
medoid: Pseudonocardia halophobica GCF 027922425 1
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AAI clade 10-11
medoid: Lentzea atacamensis GCF 003148865 1
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AAI clade 10-12
medoid: Saccharopolyspora hirsuta GCF 008630535 1
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AAI clade 10-13
medoid: Geodermatophilus siccatus GCF 900103785 1
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AAI clade 10-1
medoid: Mycolicibacterium senegalense GCF 031458155 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