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: asm GCA 900155255 1
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AAI clade 2
medoid: asm GCA 003225555 1
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AAI clade 3
medoid: miga PS19A HMP 2012 SRS017439 bin 51
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AAI clade 4
medoid: miga BA16A LX33 339
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AAI clade 5
medoid: asm GCA 002344625 1
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AAI clade 6
medoid: miga ZQ19A BG 240
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AAI clade 7
medoid: asm GCA 003220495 1
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AAI clade 8
medoid: asm GCA 001768045 1
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AAI clade 9
medoid: miga ZQ19A BG 239
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AAI clade 10
medoid: asm GCA 002508675 1
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AAI clade 11
medoid: miga PU18A 2609459660
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AAI clade 12
medoid: asm GCA 003662385 1
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AAI clade 13
medoid: asm GCA 002869845 2
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AAI clade 14
medoid: miga ZQ19A BG 334
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AAI clade 15
medoid: miga PS19A CM periimplantitis SP 502SPI T016 bin 11
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AAI clade 16
medoid: asm GCA 003218215 1
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AAI clade 17
medoid: gb PMWP00000000
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AAI clade 18
medoid: miga PS19A FerrettiP 2018 CA C10052MS2906SK t0M15 bin 9
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AAI clade 19
medoid: miga ZQ19A BG 192
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AAI clade 20
medoid: asm GCA 003222055 1
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AAI clade 21
medoid: asm GCA 002304435 1
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AAI clade 22
medoid: gb PMOA00000000
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AAI clade 23
medoid: asm GCA 001180165 1
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AAI clade 24
medoid: asm GCA 900155275 1
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AAI clade 25
medoid: asm GCA 003562785 1
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AAI clade 26
medoid: miga PS19A FengQ 2015 SID531281 bin 23
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AAI clade 27
medoid: miga PS19A XieH 2016 YSZC12003 37277 bin 27
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AAI clade 28
medoid: miga PS19A CM madagascar A27 02 1FE bin 15
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AAI clade 29
medoid: asm GCA 900317055 1
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AAI clade 30
medoid: gb MERW00000000
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AAI clade 31
medoid: miga PS19A HMP 2012 SRS011126 bin 64
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AAI clade 32
medoid: asm GCA 002320005 1
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AAI clade 33
medoid: asm GCA 900318825 1
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AAI clade 34
medoid: miga BA16A 35 5E
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AAI clade 35
medoid: miga PS19A Bengtsson PalmeJ 2015 TRAVELRES36 bin 65
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AAI clade 36
medoid: asm GCA 001604115 1
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AAI clade 37
medoid: miga SW19B 10676 0045 idba bin 101
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AAI clade 38
medoid: miga BA16A 35 12A
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AAI clade 39
medoid: miga SW19B 10678 0025 idba bin 69
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AAI clade 40
medoid: asm GCA 002372655 1
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AAI clade 41
medoid: miga ZQ19A BG 670
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AAI clade 42
medoid: asm GCA 002732585 1
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AAI clade 43
medoid: gb MFTG00000000
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AAI clade 44
medoid: asm GCF 000217915 1
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AAI clade 45
medoid: miga SW19B 10676 0006 idba bin 64
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AAI clade 46
medoid: asm GCA 005503595 1
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AAI clade 47
medoid: miga PS19A BritoIL 2016 W1 5 ST bin 1
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AAI clade 48
medoid: miga PS19A ZellerG 2014 CCIS38765456ST 20 0 bin 96
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AAI clade 49
medoid: asm GCA 002787475 1
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AAI clade 50
medoid: asm GCA 002411275 1
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AAI clade 51
medoid: asm GCA 001003965 1
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AAI clade 52
medoid: asm GCA 900315795 1
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AAI clade 53
medoid: asm GCA 002782265 1
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AAI clade 54
medoid: asm GCA 002506275 1
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AAI clade 55
medoid: asm GCA 002501805 1
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AAI clade 56
medoid: miga PS19A HMP 2012 SRS024289 bin 35
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AAI clade 57
medoid: asm GCA 002362915 1
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AAI clade 58
medoid: miga PS19A FerrettiP 2018 CA C10031IS2534SA t2M15 bin 2
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AAI clade 59
medoid: asm GCA 002478295 1
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AAI clade 60
medoid: miga PS19A HMP 2012 SRS019127 bin 5
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AAI clade 61
medoid: asm GCA 002373045 1
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AAI clade 62
medoid: gb PLQF00000000
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AAI clade 63
medoid: asm GCA 002352835 1
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AAI clade 64
medoid: miga PS19A FengQ 2015 SID31700 bin 66
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AAI clade 65
medoid: miga PS19A FerrettiP 2018 CA C10052MS2903SA t0M16 bin 3
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AAI clade 66
medoid: miga PS19A Bengtsson PalmeJ 2015 TRAVELRES6 bin 23
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AAI clade 67
medoid: miga SW19B 10678 0003 idba bin 42
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AAI clade 68
medoid: miga PS19A BritoIL 2016 M1 3 ST bin 29
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AAI clade 69
medoid: miga PS19A ZeeviD 2015 PNP Main 426 megahit bin 27
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AAI clade 70
medoid: asm GCA 002369075 1
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AAI clade 71
medoid: miga SW19B 10675 0017 idba bin 79
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AAI clade 72
medoid: miga PS19A CM madagascar V53 02 1FE bin 36
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AAI clade 73
medoid: miga PS19A RampelliS 2015 H1 bin 24
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AAI clade 74
medoid: miga PS19A HMP 2012 SRS024138 bin 26
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AAI clade 75
medoid: asm GCA 002294525 1
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AAI clade 76
medoid: miga PS19A BritoIL 2016 WL 32 ST bin 18
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AAI clade 76-1
medoid: asm GCA 002453475 1
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AAI clade 76-2
medoid: asm GCA 002306535 1
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AAI clade 76-3
medoid: miga PS19A XieH 2016 YSZC12003 37337 bin 70
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AAI clade 76-4
medoid: asm GCA 002386045 1
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AAI clade 76-5
medoid: asm GCA 002431675 1
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AAI clade 76-6
medoid: miga PS19A FengQ 2015 SID31009 bin 45
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AAI clade 76-7
medoid: miga PS19A BackhedF 2015 SID345 4M bin 6
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AAI clade 76-8
medoid: asm GCA 002329295 1
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AAI clade 76-9
medoid: miga PS19A FerrettiP 2018 CA C10024IS2415FE t3M15 bin 11
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AAI clade 76-10
medoid: miga PS19A FengQ 2015 SID31416 bin 30
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AAI clade 76-11
medoid: miga PS19A GeversD 2014 SKSTL0004 bin 39
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AAI clade 76-12
medoid: asm GCA 900314295 1
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AAI clade 76-13
medoid: miga PS19A BritoIL 2016 WL 32 ST bin 18
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AAI clade 76-14
medoid: asm GCA 002367105 1
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AAI clade 76-15
medoid: asm GCA 002308955 1
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AAI clade 76-16
medoid: miga PS19A VogtmannE 2016 MMRS77487595ST 27 0 0 bin 80
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AAI clade 76-17
medoid: miga PS19A LeChatelierE 2013 MH0086 bin 2
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AAI clade 76-18
medoid: miga PS19A Bengtsson PalmeJ 2015 TRAVELRES36 bin 12
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AAI clade 76-19
medoid: miga PS19A BritoIL 2016 W1 1 ST bin 26
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AAI clade 76-20
medoid: asm GCA 002369135 1
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AAI clade 76-21
medoid: miga PS19A CosteaPI 2017 SID713B073 11 90 0 bin 22
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AAI clade 76-22
medoid: miga SW19B 10676 0046 idba bin 80
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AAI clade 76-23
medoid: asm GCA 900319565 1
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AAI clade 76-24
medoid: miga SW19B 10674 min2k bin 3427
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AAI clade 76-25
medoid: miga PS19A HeQ 2017 SZAXPI029501 104 bin 32
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AAI clade 76-26
medoid: miga SW19B 10678 0032 idba bin 60
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AAI clade 76-27
medoid: miga SW19B 10677 0023 idba bin 105
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AAI clade 76-28
medoid: miga PS19A GeversD 2014 SKBSTL007 bin 24
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AAI clade 76-29
medoid: miga SW19B 10674 0009 idba bin 168
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AAI clade 76-30
medoid: miga PS19A KarlssonFH 2013 S488 bin 63
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AAI clade 76-31
medoid: asm GCA 002374095 1
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AAI clade 76-32
medoid: miga PS19A QinJ 2012 T2D 092 bin 49
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AAI clade 76-33
medoid: asm GCA 900315305 1
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AAI clade 76-34
medoid: miga SW19B 10674 0017 idba bin 92
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AAI clade 76-35
medoid: miga PS19A QinJ 2012 T2D 081 bin 2
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AAI clade 76-36
medoid: miga SW19B 10674 min2k bin 1331
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AAI clade 76-37
medoid: miga PS19A ZeeviD 2015 PNP Main 463 megahit bin 34
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AAI clade 76-38
medoid: miga PS19A LiJ 2014 MH0382 bin 33
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AAI clade 76-39
medoid: miga SW19B 10678 0049 idba bin 30
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AAI clade 76-40
medoid: miga PS19A Bengtsson PalmeJ 2015 TRAVELRES66 bin 78
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AAI clade 76-41
medoid: miga PS19A BritoIL 2016 M2 46 ST bin 82
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AAI clade 76-42
medoid: asm GCA 900315945 1
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AAI clade 76-43
medoid: asm GCA 001797235 1
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AAI clade 76-44
medoid: miga PS19A HMP 2012 SRS018591 bin 25
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AAI clade 76-45
medoid: miga PS19A YuJ 2015 SZAXPI003416 4 bin 10
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AAI clade 76-46
medoid: miga PS19A HeQ 2017 SZAXPI029500 102 bin 10
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AAI clade 76-47
medoid: miga PS19A ZellerG 2014 CCMD35802077ST 21 0 bin 16
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AAI clade 76-48
medoid: miga PS19A HMP 2012 SRS044662 bin 40
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AAI clade 76-49
medoid: miga PS19A HeQ 2017 SZAXPI029494 94 bin 5
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AAI clade 76-50
medoid: miga SW19B 10676 0016 idba bin 14
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AAI clade 76-51
medoid: miga SW19B 10676 min2k bin 122
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AAI clade 76-52
medoid: miga SW19B 10675 min2k bin 1778
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AAI clade 76-53
medoid: miga SW19B 10674 0017 idba bin 98
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AAI clade 76-54
medoid: miga PS19A HMP 2012 SRS049389 bin 7
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AAI clade 76-55
medoid: miga PS19A QinJ 2012 DOM012 bin 28
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AAI clade 76-56
medoid: miga PS19A Bengtsson PalmeJ 2015 TRAVELRES50 bin 54
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AAI clade 76-57
medoid: miga PS19A BackhedF 2015 SID103 4M bin 4
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AAI clade 76-58
medoid: miga PS19A NielsenHB 2014 V1 UC16 0 bin 12
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AAI clade 76-59
medoid: miga PS19A ZellerG 2014 CCIS44743950ST 4 0 bin 43
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AAI clade 76-59-1
medoid: miga SW19B 10677 min2k bin 2421
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AAI clade 76-59-2
medoid: miga PS19A CosteaPI 2017 SID713A012 11 0 0 bin 47
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AAI clade 76-59-3
medoid: miga PS19A QinN 2014 LD 35 bin 52
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AAI clade 76-59-4
medoid: miga PS19A HeQ 2017 SZAXPI029462 133 bin 22
3 datasets: miga PS19A HeQ 2017 SZAXPI029462 133 bin 22 (AAI: 100.0%), miga PS19A HeQ 2017 SZAXPI029464 140 bin 52 (AAI: 94.76%), and miga PS19A ZellerG 2014 CCIS44743950ST 4 0 bin 43 (AAI: 96.93%)
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AAI clade 76-59-5
medoid: miga PS19A ZeeviD 2015 PNP Main 255 megahit bin 6
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AAI clade 76-59-6
medoid: miga PS19A ZellerG 2014 CCIS76845094ST 20 0 bin 96
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AAI clade 76-59-1
medoid: miga SW19B 10677 min2k bin 2421
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AAI clade 76-60
medoid: miga PS19A BritoIL 2016 W1 1 ST bin 7
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AAI clade 76-61
medoid: miga PS19A FengQ 2015 SID530172 bin 44
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AAI clade 76-62
medoid: miga PS19A BackhedF 2015 SID238 M bin 26
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AAI clade 76-63
medoid: miga PS19A BackhedF 2015 SID128 M bin 40
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AAI clade 76-64
medoid: miga PS19A XieH 2016 YSZC12003 36116 bin 21
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AAI clade 76-65
medoid: miga PS19A HMP 2012 SRS015215 bin 44
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AAI clade 76-66
medoid: miga PS19A ZeeviD 2015 PNP Main 294 megahit bin 63
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AAI clade 76-67
medoid: miga PS19A BackhedF 2015 SID345 4M bin 14
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AAI clade 76-68
medoid: miga PS19A BackhedF 2015 SID526 12M bin 28
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AAI clade 76-69
medoid: miga PS19A HeQ 2017 RSZAXPI003099 133 bin 50
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AAI clade 76-70
medoid: miga PS19A HeQ 2017 SZAXPI029494 94 bin 3
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AAI clade 76-71
medoid: miga PS19A BackhedF 2015 SID590 4M bin 15
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AAI clade 76-72
medoid: miga PS19A Bengtsson PalmeJ 2015 TRAVELRES17 bin 52
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AAI clade 76-73
medoid: miga PS19A ZellerG 2014 CCMD88272491ST 21 0 bin 3
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AAI clade 76-74
medoid: miga PS19A LeChatelierE 2013 MH0406 bin 87
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AAI clade 76-75
medoid: miga PS19A Bengtsson PalmeJ 2015 TRAVELRES57 bin 43
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AAI clade 76-76
medoid: miga PS19A BritoIL 2016 M2 3 ST bin 71
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AAI clade 76-77
medoid: miga PS19A CM periimplantitis SP 261SPT T016 bin 14
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AAI clade 76-78
medoid: miga PS19A FengQ 2015 SID530373 bin 78
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AAI clade 76-79
medoid: miga PS19A LeChatelierE 2013 MH0097 bin 6
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AAI clade 76-80
medoid: miga PS19A VincentC 2016 MM058 1 megahit bin 20
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AAI clade 76-81
medoid: miga PS19A VogtmannE 2016 MMRS15137911ST 27 0 0 bin 41
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AAI clade 76-82
medoid: miga PS19A FengQ 2015 SID531766 bin 2
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AAI clade 76-83
medoid: miga PS19A HeQ 2017 RSZAXPI003082 116 bin 1
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AAI clade 76-84
medoid: miga PS19A HMP 2012 SRS016037 bin 1
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AAI clade 76-85
medoid: miga PS19A LoombaR 2017 SID5639 uuc bin 37
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AAI clade 76-1
medoid: asm GCA 002453475 1
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AAI clade 77
medoid: miga PS19A LeChatelierE 2013 MH0333 bin 59
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AAI clade 78
medoid: miga SW19B 10677 0035 idba bin 49
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AAI clade 79
medoid: miga PS19A XieH 2016 YSZC12003 37293 bin 71
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AAI clade 80
medoid: miga PS19A ZeeviD 2015 PNP Main 401 megahit bin 4
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AAI clade 81
medoid: miga PS19A OhJ 2014 MET0095 bin 1
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AAI clade 82
medoid: miga PS19A BritoIL 2016 M1 59 ST bin 42
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AAI clade 83
medoid: miga PS19A VincentC 2016 MM027 2 megahit bin 14
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AAI clade 84
medoid: asm GCA 003020965 1
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AAI clade 85
medoid: miga PS19A CosteaPI 2017 daisy 11 386 0 bin 19
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AAI clade 86
medoid: miga PS19A HMP 2012 SRS023595 bin 63
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AAI clade 87
medoid: asm GCA 001701225 1
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AAI clade 88
medoid: miga SW19B 10676 0021 idba bin 107
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AAI clade 89
medoid: miga SW19B 10678 0026 idba bin 16
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AAI clade 90
medoid: miga PS19A Bengtsson PalmeJ 2015 TRAVELRES2 bin 43
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AAI clade 91
medoid: miga PS19A VogtmannE 2016 MMRS43563715ST 27 0 0 bin 27
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AAI clade 92
medoid: miga SW19B 10674 0007 idba bin 173
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AAI clade 93
medoid: miga PS19A VatanenT 2016 G80490 bin 1