24:null 25:["$","title",null,{"children":"Computing Root-to-Tip Distances with Phylotree.js | Steven Weaver | Observable"}] 2a:T49e2,nwk = "(Jeddah-1_KF917527_camel_2013-11-08:0.0000013865,Jeddah-1_KF958702_human_2013-11-05:0.0000013652,((((Riyadh_3_2013_KF600613_human_2013-02-05:0.0006547104,(Riyadh_4_2013_KJ156952_human_2013-03-01:0.0003442202,(((((((((((((((((((D1164.1_14_KX108937_camel_2014-06-02:0.0000681430,UAE_D1164.11_2014_KP719929_camel_2014-06:0.0000013157):0.0000683541,UAE_D1164.9_2014_KP719927_camel_2014-06:0.0001028662):0.0000013586,UAE_D1164.14_2014_KP719930_camel_2014-06:0.0000015652):0.0000015652,UAE_D1164.10_2014_KP719928_camel_2014-06:0.0000336153):0.0003786069,(AbuDhabi_UAE_9_2013_KP209312_human_2013-11-15:0.0002062531,Oman_2285_2013_KT156560_human_2013-10-28:0.0001374678):0.0000014963):0.0000681046,(((KFU-HKU13_KJ650295_camel_2013-12-30:0.0000000000,KFU-HKU1_KJ650297_camel_2013-11-30:0.0000000000):0.0000015652,KFU-HKU19Dam_KJ650296_camel_2013-12-30:0.0000015652):0.0001374611,Oman_2874_2013_KT156561_human_2013-12-28:0.0003785003):0.0001025960):0.0002063627,(((AbuDhabi_Gayathi_UAE_2_2014_KP209310_human_2014-03-07:0.0002741386,(AbuDhabi_UAE_16_2014_KP209308_human_2014-04-10:0.0000681077,(((AbuDhabi_UAE_18_2014_KP209307_human_2014-04-10:0.0000680488,AbuDhabi_UAE_26_2014_KP209313_human_2014-04-13:0.0000335769):0.0000015652,(AbuDhabi_UAE_30_2014_KP209309_human_2014-04-19:0.0000015652,AbuDhabi_UAE_33_2014_KP209311_human_2014-04-17:0.0000015652):0.0000012702):0.0000208018,AbuDhabi_UAE_8_2014_KP209306_human_2014-04-07:0.0000015652):0.0000129871):0.0001030085):0.0002518240,((((D252_15_KX108939_camel_2015-01-30:0.0000015652,(D2597.2_14_KX108938_camel_2014-12-13:0.0000681309,D383_15_KX108941_camel_2015-02-14:0.0001375519):0.0000015652):0.0000683362,D374_15_KX108940_camel_2015-02-12:0.0000336152):0.0000015244,D389_15_KX108942_camel_2015-02-15:0.0001375382):0.0003786838,UAE_D1209_2014_KP719933_camel_2014-06:0.0001033123):0.0002298176):0.0000677758,(((UAE_D1243.12_2014_KP719932_camel_2014-06:0.0001030561,UAE_D1339.2_2014_KP719931_camel_2014-06:0.0000015652):0.0004471089,UAE_D511-14_KU242423_camel_2014-03-12:0.0000013387):0.0000337804,UAE_D469-14_KU242424_camel_2014-03-04:0.0000015349):0.0001613309):0.0001478654):0.0000677853,UAE-FRA1_1627-2013_BAL_KJ361500_human_2013-04-26:0.0004166820):0.0000015564,Taif_2_2013_KJ156896_human_2013-06-12:0.0002560278):0.0000669742,Asir_2_2013_KJ156863_human_2013-08-05:0.0006435122):0.0000018875,KSA-376_KJ713299_camel_2013-11:0.0006202754):0.0001017877,Buraidah_1_2013_KF600630_human_2013-05-13:0.0001722621):0.0000675496,(((((((((((Al-Hasa_11_2013_KF600629_human_2013-05-03:0.0000729341,Al-Hasa_14_2013_KF600615_human_2013-05-08:0.0001363118):0.0000010000,Al-Hasa_8_2013_KF600618_human_2013-05-01:0.0005074052):0.0000015652,Al-Hasa_21_2013_KF600634_human_2013-05-30:0.0000678122):0.0000015652,(Al-Hasa_25_2013_KJ156866_human_2013-05-02:0.0000682185,Al-Hasa_2_2013_KF186566_human_2013-04-21:0.0000335630):0.0000015652):0.0000015652,((Al-Hasa_16_2013_KF600644_human_2013-05-12:0.0000672722,Al-Hasa_7_2013_KF600623_human_2013-05-01:0.0000360478):0.0000015652,(Al-Hasa_17_2013_KF600647_human_2013-05-15:0.0001026309,((Al-Hasa_19_2013_KF600632_human_2013-05-23:0.0000015652,Al-Hasa_26_2013_KJ156882_human_2013-06-18:0.0000015652):0.0000015652,(Al-Hasa_27_2013_KJ156943_human_2013-06-19:0.0000015652,Al-Hasa_28_2013_KJ156887_human_2013-06-22:0.0002410107):0.0000018448):0.0000684495):0.0000337738):0.0000013526):0.0000015652,((((Al-Hasa_12_2013_KF600627_human_2013-05-07:0.0000000000,Al-Hasa_3_2013_KF186565_human_2013-04-22:0.0000000000):0.0000000000,Al-Hasa_1_2013_KF186567_human_2013-05-09:0.0000000000):0.0000000000,Al-Hasa_4_2013_KF186564_human_2013-05-01:0.0000000000):0.0000015652,Al-Hasa_18_2013_KF600651_human_2013-05-23:0.0000015652):0.0000015652):0.0000019804,Al-Hasa_15_2013_KF600645_human_2013-05-11:0.0000335705):0.0002574608,Al-Hasa_23_2013_KJ156860_human_2013-05-13:0.0003483095):0.0001807344,Riyadh_9_2013_KJ156869_human_2013-07-17:0.0007494948):0.0000769525,((England_2_2013_KM015348_human_2013-02-10:0.0000015652,England_3_2013_KM210278_human_2013-02-10:0.0000015652):0.0000014958,England_4_2013_KM210277_human_2013-02-13:0.0000341291):0.0003443391):0.0000332406,Riyadh_2_2012_KF600652_human_2012-10-30:0.0000682762):0.0000682702):0.0000514477,((Germany3_UAE-Dubai_Abu-Dhabi__human_2015-03-11:0.0014665018,((Indiana_USA-1_SaudiArabia_2014_KJ813439_human_2014-04-30:0.0000018734,Riyadh_2014KSA_683_KSA_2014_KM027262_human_2014-04-22:0.0001719148):0.0001028002,(((((KFMC-10_KT121578_human_2014-05-01:0.0003094681,KFMC-2_KT121577_human_2014-05-11:0.0000335879):0.0000013795,(((KFMC-1_KT121580_human_2014-04-28:0.0000000000,KFMC-4_KT121575_human_2014-05-12:0.0000000000):0.0000000000,KFMC-5_KT121572_human_2014-05-12:0.0000000000):0.0000015652,(KFMC-3_KT121573_human_2014-05-09:0.0000015652,(KFMC-7_KT121581_human_2014-05-03:0.0001718283,KFMC-8_KT121579_human_2014-04-30:0.0001718782):0.0000015652):0.0000012631):0.0000015652):0.0000018738,KFMC-6_KT121576_human_2014-05-18:0.0000335956):0.0000335956,KFMC-9_KT121574_human_2014-05-07:0.0000335959):0.0000013447,((Riyadh-KKUH-291__human_2014-05-06:0.0000015652,Riyadh-KKUH-90b__human_2014-04-24:0.0000015652):0.0000013764,Riyadh-KKUH-368__human_2014-05-13:0.0000732462):0.0000676128):0.0000337904):0.0007663463):0.0001724821,((((Hafr-Al-Batin_1_2013_KF600628_human_2013-06-04:0.0000678929,(((((((((((((Jeddah-KSA-C20860_2015_KT806055_human_2015-02-10:0.0000680505,(Jeddah_Jd175_2015_KT368866_camel_2015-02:0.0000015652,Jeddah_Jd199_2015_KT368867_camel_2015-02:0.0000015652):0.0001725222):0.0001372461,Taif_KSA-7032_2014_KU710264_human_2014-11-04:0.0003086397):0.0000017692,Jeddah_O47b_2014_KT368852_camel_2014-10:0.0002064430):0.0000013716,(((Jeddah_401_2014_KT368827_camel_2014-09:0.0000015652,Jeddah_S94_2014_KT368856_camel_2014-09:0.0000015652):0.0000337478,Jeddah_S99_2014_KT368857_camel_2014-09:0.0000334410):0.0002753790,Taif_T157b_2015_KT368890_camel_2015-03:0.0002408827):0.0000013583):0.0000014670,(((Jeddah_D100_2014_KT368828_camel_2014-12:0.0000015652,Jeddah_D88_2014_KT368843_camel_2014-12:0.0000015652):0.0000015652,Jeddah_D90_2014_KT368844_camel_2014-12:0.0000343409):0.0000333211,Jeddah_D92_2014_KT368845_camel_2014-12:0.0000685877):0.0003445798):0.0001022332,((((Jeddah_O23b_2014_KT368849_camel_2014-10:0.0000015652,Jeddah_O24_2014_KT368850_camel_2014-10:0.0000015652):0.0000013349,(Jeddah_S100_2014_KT368853_camel_2014-09:0.0002064227,Jeddah_S73_2014_KT368854_camel_2014-09:0.0000343353):0.0000343535):0.0000015652,Jeddah_O30_2014_KT368851_camel_2014-10:0.0000343400):0.0001371717,Jeddah_S93_2014_KT368855_camel_2014-09:0.0002064151):0.0001026156):0.0003091634,Riyadh_Ry23N_2014_KT368825_camel_2014-07:0.0005867518):0.0001031772,(Riyadh-KKUH-104__human_2014-04-25:0.0000015652,Riyadh-KKUH-105__human_2014-04-25:0.0000015652):0.0002403523):0.0002060409,((((Khobar-KSA-6736_2015_KT806048_human_2015-02-07:0.0004138909,((((((((Jordan_10_2015_KU233362_human_2015-09-17:0.0002067447,Jordan_1_2015_KU233363_human_2015-09-17:0.0000334657):0.0000688737,(Riyadh-KSA-16098_2015_KU851864_human_2015-08-24:0.0001024039,(Riyadh-KSA-16117_2015_KU851862_human_2015-08-24:0.0000342432,Riyadh-KSA-16120_2015_KU851861_human_2015-08-24:0.0000017352):0.0000684878):0.0001372719):0.0000014613,Riyadh-KSA-16121_2015_KU851860_human_2015-08-24:0.0001720448):0.0003443906,(Riyadh-KSA-3181_2015_KT806049_human_2015-02-15:0.0000684255,((((Riyadh_KKUH_0734__human_2015-02-18:0.0000334526,(((((Riyadh_KKUH_0780__human_2015-02-25:0.0000015652,Riyadh_KKUH_1066__human_2015-03-03:0.0000015652):0.0000015652,Riyadh_KKUH_1145__human_2015-03-04:0.0000334554):0.0000015652,((Riyadh_KKUH_0801__human_2015-02-27:0.0000015652,((Riyadh_KKUH_0939__human_2015-03-02:0.0000015652,Riyadh_KKUH_1217__human_2015-03-04:0.0001353637):0.0000016483,Riyadh_KKUH_1522__human_2015-03-09:0.0001116944):0.0000015652):0.0000378025,Riyadh_KKUH_1461__human_2015-03-08:0.0001793445):0.0000010000):0.0001021769,Riyadh_KKUH_0818__human_2015-02-28:0.0004910962):0.0000015762,((Riyadh_KKUH_0826__human_2015-02-28:0.0000367162,Riyadh_KKUH_0944__human_2015-03-02:0.0000697595):0.0000019340,Riyadh_KKUH_1470__human_2015-03-08:0.0000015652):0.0000334517):0.0000337768):0.0000342503,Riyadh_KSA_2959_2015_KT026453_human_2015-02-10:0.0000017602):0.0000014548,(Riyadh_KKUH_0755__human_2015-02-23:0.0002100374,Riyadh_KKUH_0756__human_2015-02-23:0.0000228365):0.0000123592):0.0001031838,Riyadh_KKUH_1080__human_2015-03-03:0.0002147599):0.0001029258):0.0000683696):0.0000013716,((Jeddah_D38b_2014_KT368833_camel_2014-12:0.0000013784,Jeddah_D40_2014_KT368834_camel_2014-12:0.0001369195):0.0000013865,Taif_T150_2015_KT368889_camel_2015-03:0.0002065792):0.0001368073):0.0000685592,((((((((Jeddah_D42_2014_KT368835_camel_2014-12:0.0000000000,Jeddah_D49_2014_KT368841_camel_2014-12:0.0000000000):0.0000000000,Jeddah_N68b_2014_KT368848_camel_2014-11:0.0000000000):0.0000000000,Jeddah_D48_2014_KT368840_camel_2014-12:0.0000000000):0.0000000000,Jeddah_D47_2014_KT368839_camel_2014-12:0.0000000000):0.0000000000,Jeddah_N51_2014_KT368846_camel_2014-11:0.0000000000):0.0000015652,((((Jeddah_D43b_2014_KT368836_camel_2014-12:0.0000012634,Jeddah_D46b_2014_KT368838_camel_2014-12:0.0000012635):0.0000687729,Jeddah_N62b_2014_KT368847_camel_2014-11:0.0000335319):0.0000016230,Jeddah_D45_2014_KT368837_camel_2014-12:0.0000015652):0.0000013044,Jeddah_D50b_2014_KT368842_camel_2014-12:0.0000015652):0.0000014927):0.0000013605,((((Jeddah_Jd1b_2015_KT368858_camel_2015-01:0.0000000000,Jeddah_Jd6b_2015_KT368860_camel_2015-01:0.0000000000):0.0000015652,Jeddah_Jd4_2015_KT368859_camel_2015-01:0.0000015652):0.0000013586,Jeddah_Jd7_2015_KT368861_camel_2015-01:0.0000338774):0.0000337356,(((Jeddah_Jd85_2015_KT368862_camel_2015-01:0.0000000000,Jeddah_Jd90_2015_KT368865_camel_2015-01:0.0000000000):0.0000000000,Jeddah_Jd87_2015_KT368864_camel_2015-01:0.0000000000):0.0000015652,Jeddah_Jd86_2015_KT368863_camel_2015-01:0.0000015652):0.0000338885):0.0001716494):0.0002064382,Riyadh_Ry84N_2014_KT368826_camel_2014-07:0.0005858808):0.0000019201):0.0000017295,((((((ChinaGD01_KT036372_human_2015-05-28:0.0000338455,KOR_CNUH_SNU_038_06_2015_KT868870_human_2015-06-10:0.0000342654):0.0000013125,(((((((KOR_CNUH_SNU_016_06_2015_KT868865_human_2015-06-11:0.0000000000,KOR_CNUH_SNU_085_06_2015_KT868873_human_2015-06-10:0.0000000000):0.0000000000,KOR_CNUH_SNU_030_06_2015_KT868868_human_2015-06-08:0.0000000000):0.0000015652,(KOR_CNUH_SNU_023_06_2015_KT868866_human_2015-06-11:0.0000015652,((KOR_CNUH_SNU_024_06_2015_KT868867_human_2015-06-08:0.0000015652,KOR_CNUH_SNU_031_06_2015_KT868869_human_2015-06-11:0.0000015652):0.0000018893,((KOR_CNUH_SNU_082_06_2015_KT868872_human_2015-06-10:0.0000015652,KOR_CNUH_SNU_148_06_2015_KT868876_human_2015-06-10:0.0000015652):0.0000342489,(((((KOR_CNUH_SNU_110_06_2015_KT868874_human_2015-06-11:0.0000000000,KOR_Seoul_177-3-2015_KX034100_human_2015-07-03:0.0000000000):0.0000000000,KOREA_Seoul_014-1-2015_KT374052_human_2015-05-31:0.0000000000):0.0000000000,KOR_Seoul_162-1-2015_KX034098_human_2015-06-22:0.0000000000):0.0000015652,(KOR_Seoul_077-2-2015_KX034096_human_2015-06-17:0.0000015652,KOR_Seoul_169-2015_KX034099_human_2015-06-26:0.0000687613):0.0000013044):0.0000013668,(KOREA_Seoul_035-1-2015_KT374054_human_2015-06-03:0.0000015652,Korea_Seoul_SNU1-035_2015_KU308549_human_2015-06-08:0.0000015652):0.0000685570):0.0000336305):0.0000015652):0.0000013459):0.0000012531):0.0000015652,KOR_CNUH_SNU_172_06_2015_KT868877_human_2015-06-22:0.0000015652):0.0000015652,KOR_Seoul_014-2015_KX034093_human_2015-05-30:0.0000343935):0.0000015652,KOR_CNUH_SNU_054_06_2015_KT868871_human_2015-06-09:0.0000687710):0.0000334305,((KOR_CNUH_SNU_122_06_2015_KT868875_human_2015-06-10:0.0000000000,KOR_Seoul_066-2015_KX034095_human_2015-06-04:0.0000000000):0.0000015652,(KOR_Seoul_050-1-2015_KX034094_human_2015-06-11:0.0000015652,(KOR_Seoul_080-3-2015_KX034097_human_2015-06-17:0.0000342487,KOREA_Seoul_168-1-2015_KT374056_human_2015-06-21:0.0001031546):0.0000014269):0.0000013720):0.0000336304):0.0000013563):0.0000013869,(KOR_KNIH_002_05_2015_KT029139_human_2015-05-20:0.0002745717,KOREA_Seoul_163-1-2015_KT374051_human_2015-06-19:0.0001031587):0.0000013518):0.0000013614,Hufuf-KSA-11002_2015_KT806046_human_2015-05-10:0.0000336208):0.0001720642,Riyadh_Ry159b_2015_KT368870_camel_2015-03:0.0000015555):0.0002744459,(((((((D1189.1_15_KX108946_camel_2015-05-18:0.0004133214,THA_CU_17_06_2015_KT225476_human_2015-06-17:0.0007241200):0.0000013127,D1271_15_KX108945_camel_2015-05-29:0.0003442857):0.0000013739,Hufuf-KSA-9158_2015_KT806047_human_2015-03-27:0.0003090708):0.0000335197,(((Jeddah-KSA-C20843_2015_KT806044_human_2015-02-09:0.0000342556,Jeddah-KSA-C21271_2015_KT806045_human_2015-02-22:0.0000342552):0.0000687583,Najran-KSA-C20915_2015_KT806054_human_2015-02-13:0.0000687474):0.0000013400,Riyadh_Ry79_2015_KT368878_camel_2015-03:0.0003090998):0.0000685505):0.0000013636,((Riyadh-KSA-16077_2015_KU851863_human_2015-08-27:0.0002728453,((Riyadh_Ry136_2015_KT368868_camel_2015-03:0.0000018271,(Riyadh_Ry63_2015_KT368876_camel_2015-03:0.0000013588,Riyadh_Ry64_2015_KT368877_camel_2015-03:0.0000015915):0.0000337365):0.0001368729,Riyadh_KSA_4050_2015_KT026454_human_2015-03-01:0.0001368718):0.0001046214):0.0000338402,Riyadh_Ry162_2015_KT368871_camel_2015-03:0.0003773183):0.0001401223):0.0000336132,Kharj-KSA-2598_2015_KT806053_human_2015-02-02:0.0003788599):0.0000013771,(Kharj-KSA-2599_2015_KT806052_human_2015-02-02:0.0003088110,Riyadh-KSA-3065_2015_KT806050_human_2015-02-12:0.0003401322):0.0000015652):0.0000013418):0.0000334078):0.0000349402,(((Jeddah-KSA-3RS2702_2015_KU851859_human_2015-07-12:0.0004137879,(((Taif_T16_2015_KT368882_camel_2015-04:0.0000015652,Taif_T22_2015_KT368883_camel_2015-04:0.0000015652):0.0000017071,(Taif_T3_2015_KT368880_camel_2015-04:0.0000019111,Taif_T7_2015_KT368881_camel_2015-04:0.0000019260):0.0000335244):0.0000679339,((Taif_T68_2015_KT368884_camel_2015-04:0.0000000000,Taif_T91b_2015_KT368886_camel_2015-04:0.0000000000):0.0000015652,Taif_T89_2015_KT368885_camel_2015-04:0.0000015652):0.0000015652):0.0000333132):0.0002703518,((Riyadh_Ry173_2015_KT368872_camel_2015-03:0.0001022855,Riyadh_Ry177_2015_KT368873_camel_2015-03:0.0000334153):0.0000013338,Riyadh_Ry178_2015_KT368874_camel_2015-03:0.0000334097):0.0001066623):0.0001734041,(Riyadh_Ry137_2015_KT368869_camel_2015-03:0.0000015652,Riyadh_Ry86_2015_KT368879_camel_2015-03:0.0001032234):0.0008228430):0.0001419689):0.0002050820):0.0000431365,Riyadh-KSA-2716_2015_KT806051_human_2015-02-05:0.0005098705):0.0003174862,Taif_T98_2015_KT368888_camel_2015-04:0.0005361311):0.0004952631,Taif_T92_2015_KT368887_camel_2015-04:0.0006967400):0.0001647031):0.0000690768,(Riyadh-KKUH-643__human_2014-11-02:0.0000018798,Riyadh-KKUH-665__human_2014-11-19:0.0000335156):0.0009321061):0.0000332514,((Riyadh_13_2013_KJ156888_human_2013-08-13:0.0001395990,Riyadh_14_2013_KJ156934_human_2013-08-15:0.0000015652):0.0004823180,Riyadh_7_2013_KJ156937_human_2013-07-15:0.0001752715):0.0000331448):0.0000340045,((Madinah_3b_2013_KJ156916_human_2013-09-11:0.0001469864,(Riyadh_10_2013_KJ156891_human_2013-09-05:0.0000015652,Riyadh_17_2013_KJ156918_human_2013-08-26:0.0000017782):0.0000674973):0.0001382020,(Riyadh_11_2013_KJ156946_human_2013-08-06:0.0000713825,Riyadh_8_2013_KJ156880_human_2013-07-17:0.0000015652):0.0000336866):0.0001718025):0.0000337950,(Qatar3_KF961221_human_2013-10-13:0.0000339278,Qatar4_KF961222_human_2013-10-17:0.0000015652):0.0003441489):0.0000339377):0.0001017459,Riyadh_6_2013_KJ156879_human_2013-07-02:0.0002319236):0.0001562648,(((Hafr-Al-Batin_2_2013_KJ156910_human_2013-08-05:0.0000013708,(Hafr-Al-Batin_6_2013_KJ156874_human_2013-08-28:0.0000015652,Riyadh_12_2013_KJ156926_human_2013-08-08:0.0000015652):0.0000015349):0.0000018640,Hafr-Al-Batin_5_2013_KJ156951_human_2013-08-25:0.0002210349):0.0001348925,Hafr-Al-Batin_4_2013_KJ156931_human_2013-08-25:0.0001664283):0.0003295699):0.0001551688,Jeddah_F13A_2014_KT368824_camel_2014-05:0.0012464693):0.0002063201):0.0002906558):0.0003233034,Riyadh_1_2012_KF600612_human_2012-10-23:0.0003070235):0.0002723369,(((((Camel_Egypt_NRCE-HKU270__camel_2013-12-30:0.0000015652,Camel_Egypt_NRCE-HKU271__camel_2013-12-30:0.0000336064):0.0022395635,NRCE-HKU205_KJ477102_camel_2013-11-15:0.0023706713):0.0001058132,Egypt_NRCE-NC163_2014_KU740200_camel_2014-12-17:0.0024768112):0.0008786437,D998_15_KX108943_camel_2015-04-23:0.0038186951):0.0002925602,(EMC_2012_JX869059_human_2012-06-13:0.0011224161,Jordan-N3_2012_KC776174_human_2012-04-15:0.0012028906):0.0002867892):0.0013152010):0.0001188380,Munich_AbuDhabi_2013_KF192507_human_2013-03-22:0.0003760732):0.0001666640,((((((((D1157_15_KX108944_camel_2015-05-12:0.0005530834,(((Riyadh-KSA-2049_2015_KR011266_human_2015-01-06:0.0000000000,Riyadh-KSA-2345_2015_KR011263_human_2015-01-21:0.0000000000):0.0000015652,Riyadh-KSA-2343_2015_KR011264_human_2015-01-21:0.0000015083):0.0000013442,Riyadh-KSA-2466_2015_KR011265_human_2015-01-26:0.0000015652):0.0002759187):0.0004822763,((((Jeddah_D33b_2014_KT368829_camel_2014-12:0.0000000000,Jeddah_D36_2014_KT368832_camel_2014-12:0.0000000000):0.0000015652,Jeddah_D34_2014_KT368830_camel_2014-12:0.0000015652):0.0000337500,Jeddah_D35_2014_KT368831_camel_2014-12:0.0002411042):0.0005882950,Riyadh_Ry179_2015_KT368875_camel_2015-03:0.0006568578):0.0001711021):0.0000013434,KSA-505_KJ713295_camel_2013-11:0.0000679502):0.0000761431,KSA-378_KJ713296_camel_2013-11:0.0001976231):0.0000818377,((((((Florida_USA-2_SaudiArabia_2014_KJ829365_human_2014-05-10:0.0000342375,(Jeddah_C7149_KSA_KM027255_human_2014-04-05:0.0000015652,Makkah_C9355_KSA_Makkah_KM027261_human_2014-04-15:0.0000015652):0.0000342378):0.0000013482,Jeddah_C7569_KSA_KM027256_human_2014-04-03:0.0000015652):0.0000013037,(Jeddah_C10306_KSA_KM027260_human_2014-04-21:0.0000681414,Jeddah_C8826_KSA_KM027258_human_2014-04-12:0.0000681379):0.0000015652):0.0000015652,Jeddah_C9055_KSA_KM027259_human_2014-04-14:0.0000342377):0.0000015302,(Jeddah-KFH-285TA__human_2014-06-03:0.0000523692,(Jeddah-KFH-605TD__human_2014-06-09:0.0000015652,(((Jeddah-KFH-668TD__human_2014-06-09:0.0000015652,Jeddah-KFH-899NF__human_2014-06-16:0.0000015652):0.0000455066,Jeddah-KFH-949NSG1__human_2014-06-18:0.0000016048):0.0000915267,Jeddah_C7770_KSA_KM027257_human_2014-04-07:0.0000680278):0.0000018860):0.0000010000):0.0001002543):0.0001376041,Qatar_2_2014_KJ650098_camel_2014-02-16:0.0000683992):0.0001838717):0.0002007553,KSA-503_KJ713297_camel_2013-11:0.0007260219):0.0001013796,Riyadh_2014KSA_158_KSA_2014_KM027281_human_2014-05-20:0.0006854529):0.0002870808,KSA-363_KJ713298_camel_2013-11:0.0007216187):0.0003083506):0.0000406759,England_1_2012_KC164505_human_2012-09-11:0.0003170609):0.0001297492):0.0001714554):0.0000741157,Riyadh_5_2013_KJ156944_human_2013-07-02:0.0004073223):0.0000346358,Wadi-Ad-Dawasir_1_2013_KJ156881_human_2013-06-12:0.0004188300):0.0001658065,(Taif_1_2013_KJ156949_human_2013-06-12:0.0000019293,Taif_3_2013_KJ156938_human_2013-06-13:0.0002239389):0.0002059013):0.0002748348);"2b:[] 28:{"id":"c6b2c3c642e95a1f","slug":"computing-root-to-tip-distances-with-phylotree-js","title":"Computing Root-to-Tip Distances with Phylotree.js","thumbnail":"c8c61387270f6441eab00f7cd39b8d62988bcff8f90b30d58e54b879110cc762","access_level":"public","create_time":"$D2018-09-07T15:38:18.024Z","update_time":"$D2021-05-24T23:06:23.418Z","view_time":null,"first_public_time":"$D2018-09-17T19:48:06.000Z","has_unpublished_edits":null,"fork":false,"stars":0,"starred":false,"owner":{"type":"team","id":"0fd806e981439cd5","login":"stevenweaver","name":"Steven Weaver","avatar_url":"https://avatars-next.observableusercontent.com/90a40a91ed24ae33fd0d0bd942e9a50761d78bc8a39b3c71e8dcd0ccccfd026b","tier":"starter_2024"},"version":643,"publish_version":643,"role":null,"authored":false,"authors":[{"type":"individual","id":"c627a2eb50b546f1","login":"stevenweaver","name":"Steven Weaver","avatar_url":"https://avatars-next.observableusercontent.com/90a40a91ed24ae33fd0d0bd942e9a50761d78bc8a39b3c71e8dcd0ccccfd026b","tier":null}],"members":[{"type":"individual","id":"c627a2eb50b546f1","login":"stevenweaver","name":"Steven Weaver","avatar_url":"https://avatars-next.observableusercontent.com/90a40a91ed24ae33fd0d0bd942e9a50761d78bc8a39b3c71e8dcd0ccccfd026b","tier":null,"role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":2,"collection":{"id":"5eec13a67301e7fd","slug":"phylotree-utilities","title":"Phylotree Utilities","owner":{"id":"0fd806e981439cd5","login":"stevenweaver","name":"Steven Weaver"}},"type":"notebook","body":{"title":"Computing Root-to-Tip Distances with Phylotree.js","cells":[{"id":0,"value":"md`# Computing Root-to-Tip Distances with Phylotree.js\n\nComputing root-to-tip distances and plotting them against time can help determine whether there is a strong temporal signal within a constructed tree. It is especially common to utilize a root-to-tip vs. time plot when researching the phylodynamics of a particular virus.\n\nIf the tree exhibits a positive correlation between genetic divergence and sampling time, the dataset may be appropriate for phylogenetic molecular clock analysis.¹ We will investigate if that is the case with our supplied tree by performing linear regression on root-to-tip distances vs. collection date.\n\n`\n\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":234,"value":"md`## Selecting a newick tree\n\nHere, we will use a tree that was part of a study on the transmission of Middle East respiratory syndrome coronavirus (MERS) from camels to humans.² The coronavirus was first detected in patients from the Arabian Peninsula in 2012. The tips of the tree were annotated with both host and collection date attributes.`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":6,"value":"$2a","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":483,"value":"md `## Initial rendering of the phylogenetic tree given the newick tree`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":250,"value":"viewof height = slider({\n min: 400,\n max: 5000,\n precision: 1,\n value: 2200,\n description: \"Height\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":12,"value":"viewof width = slider({\n min: 800,\n max: 5000,\n precision: 1,\n value: 800,\n description: \"Width\"\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":16,"value":"tree = new phylotree.phylotree(nwk);","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":597,"value":"tree.getTips()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":596,"value":"rendered_tree = tree.render(\"#tree_container\", {\n height:height, \n width:width, \n 'left-right-spacing': 'fit-to-size', \n 'top-bottom-spacing': 'fit-to-size'\n});","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":161,"value":"html`\n \n

\n `","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":481,"value":"md`## Computing root-to-tip distances\n\nOnce the function root_to_tip is called given the tree object, all tips within the tree should have a new attribute entitled root_to_tip`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":153,"value":"computed_tree = {\n phylotree.rootToTip(tree)\n return tree;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":490,"value":"md`Verifying that each tip has the attribute root_to_tip`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":171,"value":"tips = computed_tree.getTips()","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":493,"value":"md`## Parsing the date from the header\n\nIn order to plot root-to-tip distances against time, we will need to parse the dates from the node names. phylotree_utils provides a convenience function, extract_dates, to extract dates from the node names and place them in new attributes, decimal_date_value and date_value, in each named node.`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":504,"value":"md`Declare a callback function to extract the dates.`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":359,"value":"date_parser = function(node) {\n const default_regexp = /([0-9]{4})-?([0-9]{2})-?([0-9]{2})$/g;\n if (tree.isLeafNode(node)) {\n if (\"name\" in node.data) {\n var location = default_regexp.exec(node.data.name);\n if (location) {\n return location[1] + location[2] + location[3];\n } else {\n const default_regexp = /([0-9]{4})-?([0-9]{2})$/g;\n var location = default_regexp.exec(node.data.name);\n if (location) {\n return location[1] + location[2] + '1';\n }\n }\n \n }\n }\n return null;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":438,"value":"tree_with_dates = phylotree.extract_dates(computed_tree, date_parser)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":353,"value":"date_and_distances = {\n const mapped = _.map(tree_with_dates.getTips(), d => {return _.pick(d.data, [\"root_to_tip\", \"decimal_date_value\", \"date_value\"])});\n \n // Filter just in case the date extractor did not always find a date from the header\n return _.filter(mapped, d => { return !_.isNull(d.decimal_date_value) })\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":506,"value":"md `## Root-to-tip linear regression`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":432,"value":"fitted_slope = phylotree.fitRootToTip(tree_with_dates)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":624,"value":"computed_tree","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":444,"value":"pred = _.map(_.map(date_and_distances, d => { return d.decimal_date_value }), function(x) {return fitted_slope[\"fit\"][\"intercept\"]+fitted_slope[\"fit\"][\"slope\"]*x;})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":254,"value":"rttplot = {\n var trace = {\n type: \"scatter\",\n mode: \"markers\",\n x: _.map(date_and_distances, d => { return d.decimal_date_value }),\n y: _.map(date_and_distances, d => { return d.root_to_tip }),\n text: _.map(date_and_distances, d => { return d.date_value }),\n marker: {\n size: 5,\n color: \"red\"\n },\n name: \"Observed\"\n }\n \n var ptrace = {\n type: \"scatter\",\n mode: \"line\",\n x: _.map(date_and_distances, d => { return d.decimal_date_value }),\n y: pred,\n marker: {\n size: 5,\n color: \"black\"\n },\n name: \"Fitted\"\n }\n \n var data = [trace, ptrace];\n \n var layout = {\n title: 'Root-to-tip vs collection date',\n width: 800,\n xaxis: {tickvals:[\"2012\", \"2013\", \"2014\", \"2015\", \"2016\"]},\n };\n \n const div = DOM.element('div');\n plotly.newPlot(div, data, layout);\n return div;\n \n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":527,"value":"{\n return html`R² = ${d3.format('.3f')(fitted_slope.fit.r2)}`\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":541,"value":"md`When inspecting R², we see that there is a reasonably strong association between genetic distances and sampling dates. We can feel confident that the tree is suitable for phylogenetic molecular clock analysis in BEAST or other programs. Determining whether to use a relaxed or strict clock may be best left to further model selection methods.`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":469,"value":"md `## Table of Root-to-Tip Distances`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":176,"value":"table(_.map(tips, tip => { return _.pick(tip, \"name\", \"root_to_tip\")})) ","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":224,"value":"md` ## References\n\n1. Rambaut, Andrew, et al. \"Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen).\" Virus evolution 2.1 (2016): vew007.\n\n2. Dudas, Gytis, et al. \"MERS-CoV spillover at the camel-human interface.\" ELife 7 (2018): e31257.\n\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":260,"value":"md`## Dependencies`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":14,"value":"html``","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":569,"value":"import {slider} from \"@jashkenas/inputs\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":186,"value":"import { table } from \"@gampleman/table\"","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":209,"value":"_ = require(\"lodash@4\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":8,"value":"d3 = require(\"d3\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":564,"value":"phylotree = require('phylotree@1.0.0')","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":256,"value":"plotly = require(\"https://cdn.plot.ly/plotly-latest.min.js\")","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W2b","stdlib":"1","titling":"auto"}} 29:"$28:body"