add dir data

4043e61e · Menardo Fabrizio · f99ed54d · 4043e61e · 4043e61e · 4043e61e
Commit 4043e61e authored 7 years ago by Menardo Fabrizio
--- a/Flu_data/nextstrain_flu_h3n2_ha_12y_timetree.new_+BL
+++ b/Flu_data/nextstrain_flu_h3n2_ha_12y_timetree.new_+BL
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anghai/N07/2007:0.102821,A/Guangdong/ST798/2008:0.451212)1:0.204716)1:0.0950068)1:0.188111)1:0.124354,(A/HongKong/2657/2007:0.394313,(A/Shanghai/N11/2007:0.52591,A/Guangdong/15/2007:0.109757,(A/Guangdong/17/2007:0,(A/Nepal/AF1106/2007:0.320246,(A/Pune/715485/2007:0.414985,(A/India/P0713435/2007:0,A/Pune/713435/2007:0)1:0.338325)1:0.1106)1:0.0384123)1:0.117971)1:0.11481)1:0.101667)1:0.361144)1:0.0922163,((((A/SriLanka/14/2008:1.09441,A/SriLanka/23/2007:0.157381)1:0.192856,(A/Lyon/1381/2007:0.533214,A/Cameroon/57/2007:0.533214)1:0.370069)1:0.208327,(A/Kenya/1599/2008:0.296584,A/Kenya/1431/2008:0.271943,A/Kenya/1/2008:0.356622,A/Kenya/1598/2008:0.293846,(A/Kenya/1436/2008:0.089888,A/Kenya/1589/2008:0.196664)1:0.0944437)1:1.45363)1:0.270805,((A/Egypt/57/2006:0.170643,(A/California/NHRC0002/2007:0.281915,A/Hanoi/Q464/2007:0.446186,(A/Hanoi/Q582/2007:0.19691,A/Hanoi/Q578/2007:0.194172)1:0.361529,(A/Taiwan/707/2007:0.320972,(A/Taiwan/825/2007:0.210841,(A/Taiwan/760/2007:0.0707056,A/Taiwan/2361/2007:0.18022)1:0.0935923)1:0.167625)1:0.377097)1:0.245333)1:0.125232,((A/Georgia/7/2007:0.576451,A/Brisbane/10/2007:0.162112)1:0.33832,((A/StPetersburg/95/2007:0.328636,A/Moscow/26/2007:0.10687)1:0.280438,((((A/Argentina/3834/2007:0.148079,A/Argentina/117/2007:0.120701)1:0.354913,(A/NorthernMarianaIslands/AF1002/2007:0.0574949,A/NorthernMarianaIslands/AF1001/2007:0)1:0.210042)1:0.0853955,((A/Guyane/13/2007:0.212438,(A/India/V0713788/2007:0.0188007,(A/India/V0713790/2007:0,A/India/K0713778/2007:0.47091)1:0.0242764)1:0.0895985)1:0.0351327,((A/Netherlands/348/2007:0.262158,A/Honduras/6374/2007:0.174547)1:0.534886,((A/Argentina/3769/2007:0,A/Astrakhan/10/2007:0.536619)1:0.303338,(A/India/N075663/2007:0,(A/Pune/76064/2007:0,(A/India/And071559/2007:0,A/Andaman/71559/2007:0)1:0.394251)1:0.265572)1:0.100737)1:0.0255332)1:0.113086)1:0.075246)1:0.0645131,(A/UlanUde/1/2007:0.321009,(A/Bangladesh/9745/2007:0.144929,(A/England/543/2007:0,A/England/8016670/2007:0.427105,A/England/544/2007:0)1:0.383122,(A/Bangladesh/4699/2007:0.0378128,((A/India/C087863/2008:0,(A/Chennai/87867/2008:0,(A/India/7881/2008:0.00821355,A/India/C087878/2008:0)1:0.0848734)1:0.136893)1:0.181234,(A/Pune/83571/2008:0.0898668,((A/Delhi/914867/2009:0.285421,A/Chennai/91335/2008:0,A/Chennai/91336/2008:0.0219028)1:0.41804,(A/India/C0817271/2008:0,A/Chennai/817271/2008:0,(A/India/C0817302/2008:0,A/Chennai/817302/2008:0)1:0.0985626)1:0.245556)1:0.465803)1:0.236473)1:0.558153)1:0.0906893)1:0.258215)1:0.132029)1:0.0218815)1:0.0675042)1:0.0333966)1:0.0947534)1:0.0953322,(A/NewYork/1095/2007:0.649045,A/Kolkata/600/2006:0.199353,(A/Tumbes/FLA0424/2008:1.03486,A/Egypt/113/2007:0.179967)1:0.334924,(A/Bahia/45/2007:0.0827679,A/RioDeJaneiro/28/2007:0.00337023)1:0.612821,((A/Washington/42/2007:0.360066,A/Kuwait/AF03/2008:0.503118)1:0.165714,(A/Mexico/24010/2008:1.12573,(A/Qatar/AF02/2008:0.120642,(A/Mexico/24012/2008:0.725333,A/Mexico/24014/2008:0.722595)1:0.238567)1:0.246701)1:0.290538)1:0.788563,(((A/Tunisia/1851/2007:0.141441,(A/Perth/142/2007:0.344804,A/Darwin/20/2007:0.361231)1:0.333256)1:0.164724,((A/Aichi/68/2007:0.121684,A/Guam/AF1043/2007:0.160013)1:0.116988,(((A/Aichi/70/2007:0,A/Johannesburg/130/2007:0.210815)1:0.083479,(A/Hanoi/BM171/2007:0.215496,A/Manhean/3/2008:1.19633)1:0.0568952)1:0.161313,(A/Christchurch/1/2007:0.235181,(A/Mexico/2312/2007:0.0436416,(A/Honduras/5560/2007:0.302245,(A/California/30/2007:0.276719,(A/Texas/63/2007:0.163925,(A/Mexico/24009/2008:0.925932,A/Arizona/9/2007:0.0655623)1:0.227041)1:0.126484)1:0.208962)1:0.0398226)1:0.15321)1:0.0643673)1:0.0541125)1:0.23724)1:0.0936764,(A/CostaRica/4082/2007:0.597521,A/NewJersey/14/2007:0.76453,(A/Malaysia/1770921/2007:0.0655678,((A/Germany/AF1863/2008:0.395477,A/Malaysia/306/2008:0.283225)1:0.195098,(A/Singapore/241/2008:0.703733,((A/Penza/55/2008:0.0986932,A/Malaysia/32/2009:0.885141)1:0.181517,(A/Malaysia/1965896/2008:0.167919,(A/Malaysia/605/2008:0,A/Aichi/115/2008:0.410678)1:0.189821)1:0.0986022)1:0.155214)1:0.15515)1:0.39012)1:0.449818,(A/Wisconsin/3/2007:0.117402,((A/Parana/319/2007:0.23335,A/Argentina/449/2007:0.0188007)1:0.273955,((A/Argentina/3888/2007:0.171844,(A/Uruguay/716/2007:0.367359,A/Santiago/10086/2007:0)1:0.169106)1:0.0456455,((A/Alupe/5875/2007:0.131165,A/RioDeJaneiro/219/2007:0.024389)1:0.152368,((A/Brazil/1619/2008:0.439694,A/Brazil/1623/2008:0.447908)1:0.279399,(A/Texas/37/2007:0.00160606,(A/Texas/35/2007:0,A/Texas/64/2007:0.0301164)1:0.0344603)1:0.259582)1:0.115432)1:0.100966)1:0.151926)1:0.213421)1:0.140625,(A/India/AF1082/2007:0.173114,(A/Colorado/UR06-0534/2007:0.134262,((A/Bangladesh/30376/2007:0.268621,(A/Nevada/5/2007:0.411854,A/NewYork/1100/2007:0.0805742)1:0.185309)1:0.074948,(A/Guyane/25/2007:0.198143,((A/Managua/41901/2007:0.162134,(A/Venezuela/8241/2007:0.0602824,A/Venezuela/9602/2007:0.120515)1:0.227793)1:0.0729688,(A/Uganda/46/2007:0.179662,(A/Managua/490201/2007:0.221723,A/Managua/361601/2007:0.0656658,(A/ElSalvador/579/2007:0.243437,A/Managua/412701/2007:0.0791664)1:0.06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A/Tokyo/15345/2015:0,A/Hamamatu-C/17/2016:0.266256)1:0.674117,(A/Brisbane/197/2015:0.513324,(A/Hyogo/1041/2015:0.0436796,(A/Singapore/INFGP-16-0739/2016:0.482668,A/Bangkok/175/2016:0.597658)1:0.246159)1:0.132888,(A/Shizuoka/34/2015:0.339696,(A/HongKong/50/2016:0.302475,A/SriLanka/61/2015:0.217602)1:0.185064,(A/Nagano-C/21/2016:0.257791,(A/Taiwan/927/2016:0.332924,A/Heilongjiang-Yichun/1567/2017:0.733335)1:0.642184)1:0.372801)1:0.165414,(((A/Yokohama/120/2016:0.280761,(A/Lao/F2884/2016:0.419976,A/Ecuador/6754/2017:0.855979,A/Vietnam/16021/2016:0.277608)1:0.298841)1:0.41772,((A/Alaska/232/2015:0,(A/Victoria/2516/2016:0.50068,(A/Austria/962252/2017:1.05229,A/Pakistan/1370/2016:0.227513)1:0.566034)1:0.315967)1:0.0618871,((A/Kanagawa/IC1615/2017:0.0518885,A/Nagano/2117/2017:0.131286)1:1.31096,(A/Osaka-C/2008/2016:0.498917,(((A/Tochigi/16153/2016:0.594798,A/Ontario/RV2414/2015:0)1:0.0269915,(A/Victoria/2517/2016:0.164124,A/Talca/14380/2016:0.294327)1:0.0290371)1:0.055701,((A/Bangladesh/4017/2016:0.364965,(A/Canberra/7/2016:0,A/HongKong/1704/2016:0.0958248)1:0.170578)1:0.181204,(((A/Ethiopia/1766/2017:0.127885,A/Roraima/146724-IEC/2017:0.141574)1:0.84257,(A/Norway/4073/2016:0.222661,A/Bangladesh/222/2016:0.167904)1:0.10919)1:0.149314,((A/Gifu/28/2016:0,A/Alaska/27/2017:0.843943)1:0.286359,((A/Bangladesh/429/2016:0,(A/Ceara/145874-IEC/2017:0.408721,A/Paris/1232/2017:0.748215,A/Taiwan/826/2016:0.0603296)1:0.112155)1:0.0999061,(A/HongKong/2398/2016:0.044649,(A/Taiwan/794/2016:0.0603919,(A/Shimane/62/2016:0.0188007,A/Gifu-C/10/2017:0.290532)1:0.255144)1:0.0882954)1:0.03883)1:0.213832)1:0.183855)1:0.182731)1:0.142273)1:0.0623572)1:0.0391582)1:0.0529017)1:0.0445339)1:0.0815907,(A/Georgia/1041/2016:0.565172,A/Oman/4800/2016:0.688376,(A/HongKong/98/2016:0.130938,A/Bahrain/801/2016:0.848255,A/Newcastle/30/2016:0.369131,((A/Antananarivo/1067/2016:0.25509,(A/Kenya/115/2016:0.725505,A/Mozambique/207/2016:0.0191395)1:0.13465)1:0.111787,(A/Oman/5217/2016:0.445682,(A/Dnipro/579/2016:0,A/Dnipro/769/2016:0.142368)1:0.100713)1:0.112845)1:0.0214182,(A/Tokyo/160298/2016:0.691173,A/Singapore/Infimh-16-0019/2016:0.455718,((A/Shimane/50/2016:0.365682,A/Philippines/7/2017:0.965956)1:0.144464,(A/Virginia/1/2017:0.477349,A/Bangladesh/3001/2016:0.145384,(A/Delaware/32/2016:0.137271,A/Washington/106/2016:0.22762)1:0.213453,(A/Suriname/1665/2016:0.0402126,(A/Suriname/1693/2016:0,A/Guyane/1/2017:0.33128)1:0.0675911)1:0.0777933)1:0.43047)1:0.0961534)1:0.124228,((A/Panama/322548/2017:1.13739,A/Norway/3806/2016:0.208571,(A/Norway/4297/2016:0.444797,(A/Norway/4051/2016:0,(A/Taiwan/1095/2016:0.206791,A/Kyiv/80/2017:0.300562,A/Philippines/2/2017:0.473047,A/Netherlands/2653/2017:0.377222)1:0.255906)1:0.179225)1:0.108744)1:0.144594,((A/SouthAfrica/R05461/2017:0.706723,A/Khmelnitsky/136/2017:0.227599)1:0.203198,(A/Greece/4/2017:0.220062,(A/Florida/51/2017:0.466518,A/BayOfPlenty/1/2017:0.17083)1:0.320279)1:0.207998,(A/Thailand/46/2017:0.596338,A/Norway/2629/2017:0.349932,A/Lund/3/2017:0.286961)1:0.412146,(A/Bangkok/35/2017:0.52888,(A/PuertoRico/12/2017:0.402136,A/Brazil/9512/2017:0.114661)1:0.137696)1:0.203081)1:0.478836)1:0.224042,(A/Netherlands/1992/2017:0.796157,A/Tanzania/4384/2017:0.979593,(A/Kanagawa/AC1611/2016:0.285958,A/Colombia/5238/2017:0.9273)1:0.364408,(A/Yamaguchi/34/2016:0.314853,A/Oman/5468/2016:0)1:0.215048,(A/SriLanka/32/2016:0.115157,(A/Pennsylvania/257/2017:0.607529,A/Guatemala/199/2017:0.44052)1:0.277648)1:0.420219,((A/Florida/23/2017:0.497052,A/Sydney/52/2017:0.450508)1:0.340008,(A/Bahrain/786/2016:0.146523,(((A/Dnipro/725/2016:0.0674184,(A/Dnipro/748/2016:0,A/Dnipro/245/2017:0.123888)1:0.0728941)1:0.270919,((A/SouthAustralia/32/2017:0.125266,A/Argentina/747/2017:0.434644)1:0.373968,(A/Kentucky/29/2016:0,(A/Wisconsin/85/2016:0,(A/Stockholm/30/2017:0.454634,A/Stockholm/28/2017:0.438207,(A/Orebro/1/2017:0.23124,(A/HongKong/4193/2017:0.268822,A/Yokohama/142/2017:0.211327)1:0.0637186)1:0.0125797)1:0.50156)1:0.104038)1:0.038591)1:0.0369125)1:0.0161734,((A/Tokyo/17176/2017:0.354364,A/SouthAfrica/R06408/2017:0.439238,(A/SouthAfrica/R07360/2017:0.408926,A/Sydney/1049/2017:0.44178)1:0.0713794,(A/Bangladesh/3039/2017:0.297399,A/Chanthaburi/36/2017:0.185147)1:0.0679169,(A/NewZealand/657/2017:0.217854,(A/NewZealand/719/2017:0.00273785,A/NewZealand/677/2017:0)1:0.228806)1:0.191267)1:0.221877,(A/Bangladesh/1234/2017:0.156864,A/SouthAustralia/70/2017:0.294713,A/Osaka/176/2017:0.516479,A/Bangladesh/2062/2017:0.511003,((A/Suphanburi/89/2017:0.165492,A/Singapore/MOH0087/2017:0.0806185,A/Tokyo/17185/2017:0.184657)1:0.165065,((A/Bangladesh/2226/2017:0.00273785,A/HongKong/3084/2017:0)1:0.173659,(A/Florida/52/2017:0.110973,A/NewJersey/30/2017:0.135613)1:0.158511)1:0.214393)1:0.120213)1:0.122733)1:0.304621)1:0.0384185)1:0.134069)1:0.0905138)1:0.422392)1:0.171401)1:0.20121)1:0.158303)1:0.251143)1:0.370108)1:0.277897)1:0.0593434)1:0.0542159)1:0.00618923)1:0.10056)1:0.0327267)1:0.0996613)1:0.10333)1:0.0953643)1:0.138919)1:0.0630804)1:0.0514854)1:0.151264)1:0.300785)1:0.290526)1:0.0784863)1:0.162179)1:0.241149)1:0.168118)1:0.156316)1:0.100511)1:0.174967)1:0.171227)1:0.0705469)1:0.0534389)1:0.0297088)1:0.0496324)1:0.0549977)1:0.11449)1:0.15584)1:0.376527)1:0.0306906)1:0.080387)1:0.0627622)1:0.076345)1:0.0383612)1:0.111146)1:0.140287)1:0.224236)1:0)1:0.142901)1:0.0838396)1:0.0746173)1:0.0599814)1:0.0994318)1:0.0646998)1:0.100187)1:0.0583833)1:0.0433149)1:0.00411864)1:0.0603494)1:0.054148)1:0.0511712)1:0.045308)1:0.303341)1:0.141851)1:0.0688965)1:0.356602)1:0.0269915)1:0.0780807)1:0.102788)1:0.11896)1:0.107837)1:0.0417452)1:0.336676)1:0.18518)1:0.112684)1:0.342717)1:0.0749207)1:0.146977)1:0.0980069)1:0.236067)1:0.455562)1:0.041077)1:0.0452017)1:0.0242044)1:0.0562581)1:1.01825);
\ No newline at end of file
--- a/Flu_data/nextstrain_flu_h3n2_ha_12y_timetree.new_+BL_res_100_LD
+++ b/Flu_data/nextstrain_flu_h3n2_ha_12y_timetree.new_+BL_res_100_LD
+0.998865940013	1980
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+0.0213840212255	5
+0.0164555128084	3
\ No newline at end of file
--- a/Flu_data/nextstrain_flu_h3n2_ha_12y_timetree.new_+BL_res_10_LD
+++ b/Flu_data/nextstrain_flu_h3n2_ha_12y_timetree.new_+BL_res_10_LD
+1.0	2070
+1.0	2060
+0.999991235966	2050
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+0.99993280907	2030
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+0.999694309389	2010
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+0.759246817665	970
+0.75547866758	960
+0.751460099184	950
+0.746462881199	940
+0.741925423137	930
+0.737320328078	920
+0.732563792686	910
+0.728350249856	900
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+0.721557708688	880
+0.717835498786	870
+0.713805941456	860
+0.710118967271	850
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+0.695268483459	820
+0.692116376307	810
+0.687948981035	800
+0.683313344726	790
+0.679891669107	780
+0.674662810789	770
+0.668793844149	760
+0.6648073963	750
+0.65968016815	740
+0.655124065561	730
+0.649974523751	720
+0.643887913538	710
+0.639965134968	700
+0.633859333948	690
+0.62903428081	680
+0.623628900859	670
+0.617082570897	660
+0.612066648985	650
+0.605571392273	640
+0.599811064852	630
+0.594386844183	620
+0.588028009368	610
+0.580609288777	600
+0.575408344381	590
+0.570369696192	580
+0.565066734192	570
+0.559238938682	560
+0.552889525881	550
+0.5464950486	540
+0.540624469157	530
+0.536666552076	520
+0.528158741118	510
+0.522613540849	500
+0.515754715667	490
+0.507774606585	480
+0.503210130152	470
+0.496590848091	460
+0.492761600036	450
+0.488884868992	440
+0.481924114234	430
+0.476370166801	420
+0.469814824615	410
+0.460684106682	400
+0.45447015962	390
+0.447585172137	380
+0.440728400544	370
+0.432847529339	360
+0.4236947581	350
+0.416812437958	340
+0.408363485292	330
+0.400304738967	320
+0.39209067945	310
+0.384266355718	300
+0.373724855487	290
+0.363354333818	280
+0.353597229674	270
+0.345928518861	260
+0.337631583145	250
+0.329900173723	240
+0.32284899057	230
+0.312108569899	220
+0.301951736111	210
+0.291994094456	200
+0.280728361183	190
+0.271548008185	180
+0.26100884153	170
+0.253047671653	160
+0.242007087168	150
+0.231168742948	140
+0.221261850542	130
+0.207483503726	120
+0.195190368333	110
+0.184636078888	100
+0.168529652746	90
+0.153747068846	80
+0.143754611625	70
+0.127343416832	60
+0.113825032941	50
+0.0960014890347	40
+0.0805575066408	30
+0.0572739124443	20
+0.0381228632856	11
+0.0269350207669	5
+0.0208513108681	3
\ No newline at end of file
--- a/Flu_data/nextstrain_flu_h3n2_ha_12y_timetree.new_+BL_res_1_LD
+++ b/Flu_data/nextstrain_flu_h3n2_ha_12y_timetree.new_+BL_res_1_LD
--- a/Flu_data/nextstrain_flu_h3n2_ha_12y_timetree.new_+BL_trimmed_list_X_250
+++ b/Flu_data/nextstrain_flu_h3n2_ha_12y_timetree.new_+BL_trimmed_list_X_250
+A/TayNguyen/TN403/2005
+A/India/P0618976/2006
+A/Hiroshima/9/2005
+A/Incheon/677/2006
+A/Iwate/40/2006
+A/Santiago/6764/2006
+A/Honduras/3112/2006
+A/CostaRica/7322/2006
+A/Dnipropetrovsk/324/2007
+A/Toulon/1244/2006
+A/Japan/54/2007
+A/Japan/44/2007
+A/Egypt/51/2006
+A/Johannesburg/245/2006
+A/Taiwan/717/2006
+A/Kenya/1599/2008
+A/SriLanka/23/2007
+A/Taiwan/707/2007
+A/UlanUde/1/2007
+A/India/C0817302/2008
+A/Netherlands/348/2007
+A/Mexico/24010/2008
+A/Mexico/24014/2008
+A/Kuwait/AF03/2008
+A/Singapore/241/2008
+A/Parana/319/2007
+A/Johannesburg/130/2007
+A/Mexico/24009/2008
+A/HunanFurong/1217/2007
+A/Victoria/500/2009
+A/Shanghai/N05/2007
+A/Sichuan/Qingyang1396/2008
+A/Taiwan/72106/2007
+A/India/C087882/2008
+A/Lyon/CHU20526/2009
+A/Gothenburg/3/2009
+A/Cheongju/H397/2008
+A/Hanoi/N317/2007
+A/Brisbane/54/2009
+A/Perth/12/2008
+A/Brisbane/24/2008
+A/Umea/1/2009
+A/KhanhHoa/KH466/2008
+A/KhanhHoa/KH363/2008
+A/Japan/677/2009
+A/Boston/20/2008
+A/Guangdong/472/2009
+A/Philippines/3967/2008
+A/Tennessee/16/2009
+A/Perth/160/2009
+A/Shanghai-Nanhui/146/2009
+A/Macau/1343/2008
+A/Shanghai/N03/2007
+A/Colombia/227/2009
+A/Madagascar/453/2009
+A/Kenya/1270/2009
+A/Kenya/1668/2008
+A/Uganda/MUWRP-042/2008
+A/Suriname/5163/2009
+A/Paris/358/2007
+A/SouthKorea/WRAIR1171P/2009
+A/MexicoCity/WRAIR1752T/2010
+A/Moscow/26/2009
+A/Perth/26/2009
+A/CaymanIslands/9266/2009
+A/Acre/26954/2010
+A/Korea/WRAIR1038P/2009
+A/Shanghai-Fengxian/1170/2011
+A/Singapore/GP3303/2009
+A/Stockholm/7/2010
+A/Guizhou-Nanming/11165/2011
+A/Jiangsu-Xinpu/1385/2012
+A/Fukuoka-C/62/2011
+A/Taiwan/42/2010
+A/NewMexico/2/2008
+A/Auckland/121/2008
+A/Boston/5/2009
+A/Japan/WRAIR1059P/2008
+A/Kyrgyzstan/WRAIR1255P/2008
+A/Guatemala/29/2009
+A/Kenya/2817/2009
+A/Stockholm/1/2010
+A/Guyane/1296/2012
+A/Tennessee/F1026/2010
+A/Alaska/5/2010
+A/Wisconsin/32/2011
+A/Tucuman/I2270/2012
+A/DistrictofColumbia/WRAIR1753P/2010
+A/Guangdong-Jinping/1334/2011
+A/Guangdong/174/2011
+A/Ontario/24/2011
+A/Perth/10/2010
+A/Peru/1026/2012
+A/Stockholm/18/2010
+A/SaoPaulo/16761/2011
+A/SaoPaulo/32892/2001
+A/Brisbane/39/2012
+A/Nicaragua/AGA2-76/2012
+A/Hiroshima-C/53/2011
+A/Connecticut/Flu139/2013
+A/Tucuman/I2042/2012
+A/Ghana/FS/10-4462/2010
+A/Malaysia/4/2013
+A/Victoria/342/2012
+A/Johannesburg/5903/2012
+A/Norway/1775/2011
+A/Dakar/21/2011
+A/Afghanistan/2950/2009
+A/Shizuoka/736/2009
+A/Kenya/230/2012
+A/Kenya/152/2011
+A/Kenya/231/2012
+A/Newcastle/4/2010
+A/Kenya/221/2012
+A/Peru/PER363/2012
+A/Bangladesh/3564/2011
+A/Cairo/134/2012
+A/Southaustralia/2/2013
+A/Cairo/152/2013
+A/Tehran/34891/2013
+A/Thailand/CU-B8127/2013
+A/Delhi/8865/2011
+A/Singapore/TT241/2011
+A/Victoria/803/2011
+A/Victoria/361/2011
+A/Victoria/527/2012
+A/Southaustralia/66/2012
+A/Boston/DOA2-109/2012
+A/Taiwan/607/2012
+A/Haryana/9972/2012
+A/Brisbane/1/2013
+A/Chanthaburi/170/2013
+A/PuertoRico/25/2014
+A/Thailand/CU-B10828/2014
+A/HongKong/7347/2014
+A/SriLanka/64/2014
+A/Perth/43/2015
+A/SouthAustralia/9/2015
+A/Indonesia/Nihrd-Dps302/2016
+A/Brisbane/1027/2017
+A/Canberra/82/2014
+A/Congo/560/2016
+A/Guyane/1742/2015
+A/SouthAfrica/R2665/2015
+A/Uganda/215/2017
+A/Bangkok/43/2015
+A/Moscow/134/2016
+A/Santiago/3142/2016
+A/SouthAfrica/4244/2015
+A/Stockholm/17/2014
+A/Gifu/46/2014
+A/Slovenia/1172/2016
+A/Peru/216/2016
+A/Yokohama/123/2016
+A/Perth/1055/2014
+A/Bratislava/184/2016
+A/NewYork/19/2014
+A/Alaska/36/2017
+A/HongKong/123/2017
+A/Gangwon/1602/2015
+A/Tokyo/15250/2015
+A/SouthAustralia/21/2015
+A/Colombia/7113/2015
+A/Mie/27/2016
+A/Kanagawa/IC1615/2017
+A/Alaska/27/2017
+A/Paris/1232/2017
+A/Norway/4073/2016
+A/Victoria/2516/2016
+A/Austria/962252/2017
+A/Ecuador/6754/2017
+A/Panama/322548/2017
+A/PuertoRico/12/2017
+A/Kanagawa/AC1611/2016
+A/Nagano-C/21/2016
+A/Hamamatu-C/17/2016
+A/Fiji/60/2016
+A/Jilin-Longshan/15/2017
+A/HongKong/3555/2017
+A/Mahasarakham/123/2017
+A/Guatemala/4084/2015
+A/Jordan/30226/2015
+A/India/609/2015
+A/Malaysia/22/2013
+A/Japan/2013
+A/Virginia/14/2014
+A/HongKong/15/2013
+A/Ghana/DILI-495/2013
+A/HongKong/1036/2013
+A/SouthAustralia/177/2012
+A/Santiago/82830/2013
+A/Norway/161/2014
+A/Philippines/12/2013
+A/Fiji/1/2014
+A/Poland/1702/2014
+A/Norway/2326/2015
+A/SouthAfrica/4371/2014
+A/Boston/YGA_00097/2013
+A/Madagascar/897/2014
+A/Utah/9/2014
+A/SaoPaulo/61715/2013
+A/Nicaragua/5892_01_TR1/2013
+A/SouthAfrica/4090/2014
+A/Navarra/618/2015
+A/SouthAfrica/4655/2013
+A/NewJersey/8/2013
+A/SriLanka/58/2014
+A/Berlin/27/2016
+A/Ghana/DILI-0658/2014
+A/Singapore/GP142/2014
+A/Guizhou-Xinyi/1799/2014
+A/Jiangsu-Sucheng/1309/2016
+A/Miyazaki/62/2014
+A/PuertoRico/13/2017
+A/Madagascar/2739/2014
+A/Liaoning-Shuangta/1491/2015
+A/NorthCarolina/13/2014
+A/Myanmar/14M240/2014
+A/Hebei-Yunhe/1101/2017
+A/Cambodia/AD04526/2014
+A/Texas/88/2016
+A/Uganda/2447/2016
+A/NewZealand/889/2016
+A/NelsonMarlborough/1/2013
+A/Guizhou-Duyun/1652/2013
+A/Thailand/CU-B6936/2012
+A/Guangdong-Dongguanbendi/1729/2011
+A/Macau/200134/2012
+A/HongKong/4937/2011
+A/Norway/1359/2012
+A/Kaliningrad/4/2012
+A/Madagascar/257/2011
+A/Egypt/N13417/2009
+A/HongKong/2571/2007
+A/Guangdong/578/2008
+A/HongKong/3049/2008
+A/Guangdong/548/2008
+A/Shanghai/N13/2007
+A/LiaoningTiedong/14/2008
+A/HeilongjiangQiqiharJianhua/1593/2009
+A/Singapore/215/2008
+A/ShanghaiPudongxin/237/2008
+A/Novosibirsk/1/2008
+A/Korea/7719/2008
+A/RioDeJaneiro/28/2007
+A/Tumbes/FLA0424/2008
+A/Canada/101/2006
+A/Singapore/57/2006
+A/NewYork/1079/2007
+A/Japan/63/2007
\ No newline at end of file
--- a/Flu_data/nextstrain_flu_h3n2_ha_12y_timetree.new_+BL_trimmed_tree_X_250
+++ b/Flu_data/nextstrain_flu_h3n2_ha_12y_timetree.new_+BL_trimmed_tree_X_250
+((A/TayNguyen/TN403/2005:1.09756,(A/India/P0618976/2006:1.41369,A/Hiroshima/9/2005:0.552116)1:0.552455,A/Incheon/677/2006:2.19339)1:0.165902,(A/Iwate/40/2006:0.804418,((A/Santiago/6764/2006:0.772385,(A/Honduras/3112/2006:1.01827,A/CostaRica/7322/2006:0.892326)1:0.329066)1:0.0496963,((((A/Dnipropetrovsk/324/2007:1.20232,(A/Toulon/1244/2006:0.447265,(A/Japan/54/2007:1.08255,A/Japan/44/2007:1.08255)1:0.148426)1:0.521655,A/Egypt/51/2006:0.979871)1:0.236245,A/Johannesburg/245/2006:0.693187)1:0.0704407,((A/Taiwan/717/2006:0.412095,(((A/Kenya/1599/2008:1.75021,A/SriLanka/23/2007:0.558564)1:0.270805,(A/Taiwan/707/2007:1.06863,((A/UlanUde/1/2007:0.321009,A/India/C0817302/2008:1.95345)1:0.132029,A/Netherlands/348/2007:1.04989)1:0.122782)1:0.0947534)1:0.0953322,(((A/Mexico/24010/2008:1.12573,A/Mexico/24014/2008:1.20786)1:0.290538,A/Kuwait/AF03/2008:0.668832)1:0.788563,((A/Singapore/241/2008:1.69882,A/Parana/319/2007:0.861351)1:0.0925323,(A/Johannesburg/130/2007:0.455607,A/Mexico/24009/2008:1.74582)1:0.385029)1:0.0739812,((((A/HunanFurong/1217/2007:0.285062,A/Victoria/500/2009:1.77582)1:0.207703,(A/Shanghai/N05/2007:0.381451,(A/Sichuan/Qingyang1396/2008:1.49765,A/Taiwan/72106/2007:0.459325)1:0.0946103)1:0.204401)1:0.116106,A/India/C087882/2008:1.39532)1:0.22535,((((A/Lyon/CHU20526/2009:0.721328,A/Gothenburg/3/2009:1.26069)1:1.23756,A/Cheongju/H397/2008:0.619391)1:0.147103,(((A/Hanoi/N317/2007:0.148117,A/Brisbane/54/2009:1.70185)1:0.194478,A/Perth/12/2008:0.956557)1:0.0970235,(((A/Brisbane/24/2008:0.789809,A/Umea/1/2009:1.37366)1:0.1663,(A/KhanhHoa/KH466/2008:0.792619,(A/KhanhHoa/KH363/2008:0.370328,A/Japan/677/2009:1.51543)1:0.227904)1:0.609761)1:0.0598382,(((A/Boston/20/2008:0.320387,A/Guangdong/472/2009:1.59144)1:0.073532,(A/Philippines/3967/2008:0.718341,A/Tennessee/16/2009:1.90451)1:0.154703)1:0.0939087,((A/Perth/160/2009:1.18993,A/Shanghai-Nanhui/146/2009:0.831272)1:0.184301,A/Macau/1343/2008:0.379708)1:0.5407)1:0.125655)1:0.108817)1:0.0934737)1:0.210294,((A/Shanghai/N03/2007:0.128981,A/Colombia/227/2009:2.00852)1:0.159489,((((A/Madagascar/453/2009:0.910495,A/Kenya/1270/2009:1.04465)1:0.0680182,A/Kenya/1668/2008:0.561674)1:0.673434,(A/Uganda/MUWRP-042/2008:1.32172,((A/Suriname/5163/2009:1.75021,A/Paris/358/2007:0.14994)1:0.0934155,(A/SouthKorea/WRAIR1171P/2009:0.767529,A/MexicoCity/WRAIR1752T/2010:1.83598)1:0.624355)1:0.0263472)1:0.121464)1:0.114588,(((A/Moscow/26/2009:0.951641,(A/Perth/26/2009:0.649933,((A/CaymanIslands/9266/2009:0.804782,A/Acre/26954/2010:1.25447)1:0.251792,(A/Korea/WRAIR1038P/2009:0.44353,(A/Shanghai-Fengxian/1170/2011:1.86823,A/Singapore/GP3303/2009:0.16118)1:0.660174)1:0.0764257)1:0.0560545,(((A/Stockholm/7/2010:0.514799,(A/Guizhou-Nanming/11165/2011:0.642446,A/Jiangsu-Xinpu/1385/2012:1.4727)1:0.820333)1:0.48764,A/Fukuoka-C/62/2011:1.31798)1:0.130484,A/Taiwan/42/2010:0.60178)1:1.0372)1:0.493358)1:0.423879,A/NewMexico/2/2008:0.580859)1:0.0926686,((A/Auckland/121/2008:0.796977,A/Boston/5/2009:1.28226)1:0.0729983,(A/Japan/WRAIR1059P/2008:0.526684,((A/Kyrgyzstan/WRAIR1255P/2008:0.71887,A/Guatemala/29/2009:1.31914)1:0.144587,(A/Kenya/2817/2009:0.602958,(A/Stockholm/1/2010:0.708228,(((A/Guyane/1296/2012:2.24732,A/Tennessee/F1026/2010:0.0803136)1:0.0767758,(A/Alaska/5/2010:0.417176,(A/Wisconsin/32/2011:0.808739,A/Tucuman/I2270/2012:1.51031)1:0.958883)1:0.334026)1:0.0900724,(A/DistrictofColumbia/WRAIR1753P/2010:0.640306,(((A/Guangdong-Jinping/1334/2011:1.09091,A/Guangdong/174/2011:1.03615)1:0.243534,A/Ontario/24/2011:0.778659)1:0.0813671,(A/Perth/10/2010:0.0755485,((A/Peru/1026/2012:2.01922,A/Stockholm/18/2010:0.249199)1:0.283049,(A/SaoPaulo/16761/2011:0.327033,((A/SaoPaulo/32892/2001:0.124058,(A/Brisbane/39/2012:1.14112,A/Nicaragua/AGA2-76/2012:1.39574)1:0.054121)1:0.197084,(A/Hiroshima-C/53/2011:0.730717,A/Connecticut/Flu139/2013:1.9915)1:0.173588)1:0.0469583,A/Tucuman/I2042/2012:1.74866)1:0.419452)1:0.134677)1:0.058263)1:0.208068)1:0.283106)1:0.154427)1:0.585353,((A/Ghana/FS/10-4462/2010:1.09336,((A/Malaysia/4/2013:2.07066,((A/Victoria/342/2012:1.18859,A/Johannesburg/5903/2012:1.16395)1:0.20117,A/Norway/1775/2011:0.433562)1:0.108013)1:0.132554,A/Dakar/21/2011:0.843876)1:1.25222)1:0.519892,(A/Afghanistan/2950/2009:0.597437,((A/Shizuoka/736/2009:0.067618,((A/Kenya/230/2012:1.39926,A/Kenya/152/2011:0.744229)1:0.394121,A/Kenya/231/2012:2.06716)1:1.20031)1:0.0332612,(((A/Newcastle/4/2010:0.282951,((A/Kenya/221/2012:1.61903,(A/Peru/PER363/2012:1.67477,(A/Bangladesh/3564/2011:0.429232,((A/Cairo/134/2012:0.978276,A/Southaustralia/2/2013:1.03646)1:0.0759552,A/Cairo/152/2013:1.09325)1:0.810319)1:0.426235)1:0.144126)1:0.192353,(A/Tehran/34891/2013:3.05616,(((A/Thailand/CU-B8127/2013:2.74485,A/Delhi/8865/2011:0.254775)1:0.187332,A/Singapore/TT241/2011:0.825406)1:0.173226,(A/Victoria/803/2011:0.686832,((A/Victoria/361/2011:0.89942,A/Victoria/527/2012:1.54624)1:0.285909,(((((A/Southaustralia/66/2012:1.08456,A/Boston/DOA2-109/2012:1.30633)1:0.126043,((A/Taiwan/607/2012:0.841218,A/Haryana/9972/2012:1.44355)1:0.107053,((((A/Brisbane/1/2013:0.76112,(A/Chanthaburi/170/2013:0.696823,((A/PuertoRico/25/2014:1.56567,(A/Thailand/CU-B10828/2014:1.20434,(A/HongKong/7347/2014:0.864587,(((A/SriLanka/64/2014:0.714313,A/Perth/43/2015:1.1996)1:0.148075,((A/SouthAustralia/9/2015:0.483925,A/Indonesia/Nihrd-Dps302/2016:1.37989)1:0.310707,A/Brisbane/1027/2017:3.2628)1:0.284731)1:0.145279,(((A/Canberra/82/2014:0.103197,(A/Congo/560/2016:1.64264,(A/Guyane/1742/2015:0.375625,((A/SouthAfrica/R2665/2015:0.314208,A/Uganda/215/2017:1.97745)1:0.036248,(A/Bangkok/43/2015:0.331328,(A/Moscow/134/2016:1.07101,A/Santiago/3142/2016:0.821869)1:0.117945)1:0.0492446)1:0.359187)1:0.0835758,A/SouthAfrica/4244/2015:0.935588)1:0.126542)1:0.153174,(A/Stockholm/17/2014:0.174676,((A/Gifu/46/2014:0.412362,(A/Slovenia/1172/2016:0.909449,(A/Peru/216/2016:1.10969,A/Yokohama/123/2016:1.06862)1:0.0653344)1:0.744528)1:0.0545199,((A/Perth/1055/2014:0.274559,A/Bratislava/184/2016:1.57093)1:0.0599502,(A/NewYork/19/2014:0.18077,(A/Alaska/36/2017:1.17554,A/HongKong/123/2017:0.666297)1:1.79716)1:0.0332737)1:0.03381)1:0.0965692)1:0.059792)1:0.0998853,(((((A/Gangwon/1602/2015:1.22342,A/Tokyo/15250/2015:0.905829)1:0.243892,(A/SouthAustralia/21/2015:0.469608,(A/Colombia/7113/2015:0.639112,A/Mie/27/2016:1.3489)1:0.558765)1:0.242056)1:0.100327,(((((((A/Kanagawa/IC1615/2017:1.36285,((A/Alaska/27/2017:1.1303,A/Paris/1232/2017:1.17411)1:0.183855,A/Norway/4073/2016:0.481165)1:0.426519)1:0.0529017,(A/Victoria/2516/2016:0.50068,A/Austria/962252/2017:1.61832)1:0.377854)1:0.0445339,A/Ecuador/6754/2017:1.57254)1:0.0815907,((A/Panama/322548/2017:1.28198,A/PuertoRico/12/2017:1.22175)1:0.224042,A/Kanagawa/AC1611/2016:1.07276)1:0.372611)1:0.158303,A/Nagano-C/21/2016:0.796006)1:0.251143,A/Hamamatu-C/17/2016:0.940373)1:0.370108,(A/Fiji/60/2016:1.14801,(A/Jilin-Longshan/15/2017:0.448299,(A/HongKong/3555/2017:0.945447,A/Mahasarakham/123/2017:0.937233)1:0.0285192)1:1.30546)1:0.534817)1:0.33724)1:0.0542159,A/Guatemala/4084/2015:1.03322)1:0.00618923,A/Jordan/30226/2015:0.960008)1:0.10056,A/India/609/2015:0.9182)1:0.331082)1:0.138919)1:0.26583)1:0.591311)1:0.0784863,A/Malaysia/22/2013:0.989126)1:0.162179)1:0.409267)1:0.156316,A/Japan/2013:1.50334)1:0.100511,(A/Virginia/14/2014:2.5516,(A/HongKong/15/2013:0.674866,(A/Ghana/DILI-495/2013:1.13456,A/HongKong/1036/2013:0.797802,(A/SouthAustralia/177/2012:0.488069,((A/Santiago/82830/2013:1.32428,(((A/Norway/161/2014:1.1369,(A/Philippines/12/2013:0.684083,A/Fiji/1/2014:1.34185)1:0.0907374,(A/Poland/1702/2014:1.23756,A/Norway/2326/2015:2.32517)1:0.134793,A/SouthAfrica/4371/2014:1.50377)1:0.058115,A/Boston/YGA_00097/2013:0.386665)1:0.0528271,((A/Madagascar/897/2014:1.15257,A/Utah/9/2014:1.31958)1:0.0643987,A/SaoPaulo/61715/2013:0.622165)1:0.178723)1:0.161989)1:0.089141,((A/Nicaragua/5892_01_TR1/2013:0.874143,((((A/SouthAfrica/4090/2014:0.687891,A/Navarra/618/2015:1.33745)1:0.330773,A/SouthAfrica/4655/2013:0.114489)1:0.630728,(A/NewJersey/8/2013:0.752015,(((A/SriLanka/58/2014:0.528228,A/Berlin/27/2016:1.76437)1:0.574746,A/Ghana/DILI-0658/2014:0.831926)1:0.0598605,(A/Singapore/GP142/2014:0.324294,((A/Guizhou-Xinyi/1799/2014:0.444708,A/Jiangsu-Sucheng/1309/2016:1.97653)1:0.352788,(A/Miyazaki/62/2014:0.445934,A/PuertoRico/13/2017:3.15025)1:0.222884)1:0.24959,((A/Madagascar/2739/2014:0.720077,A/Liaoning-Shuangta/1491/2015:1.83233)1:0.0755262,(A/NorthCarolina/13/2014:0.0997412,((A/Myanmar/14M240/2014:0.0548869,A/Hebei-Yunhe/1101/2017:2.60862)1:0.298246,(A/Cambodia/AD04526/2014:0.487592,(A/Texas/88/2016:0.93562,(A/Uganda/2447/2016:1.22279,A/NewZealand/889/2016:1.07495)1:0.493114)1:0.837394)1:0.139325)1:0.0505098)1:0.235903)1:0.232318)1:0.0555148)1:0.67953)1:0.247822)1:0.0632079,A/NelsonMarlborough/1/2013:1.09316)1:0.0465538)1:0.0610703,A/Guizhou-Duyun/1652/2013:1.10496)1:0.031932)1:0.110245)1:0.0681178)1:0.0447575)1:0.0765951)1:0.243899)1:0.174967,A/Thailand/CU-B6936/2012:0.888328)1:0.429552)1:0.11449)1:0.15584,A/Guangdong-Dongguanbendi/1729/2011:0.569046)1:0.376527,A/Macau/200134/2012:1.33229,(A/HongKong/4937/2011:0.751589,A/Norway/1359/2012:1.20676)1:0.423962)1:0.0306906,A/Kaliningrad/4/2012:1.59297)1:0.080387)1:0.0627622)1:0.076345)1:0.0383612)1:0.111146)1:0.140287)1:0.749707,A/Madagascar/257/2011:1.63293)1:0.100187,A/Egypt/N13417/2009:0.650299)1:0.0583833)1:0.107783)1:0.054148)1:0.0964792)1:0.975763)1:0.221748)1:0.107837)1:0.0417452)1:0.336676)1:0.18518)1:0.112684)1:0.342717,(A/HongKong/2571/2007:0.597252,(A/Guangdong/578/2008:1.66348,A/HongKong/3049/2008:1.63336,A/Guangdong/548/2008:1.73193)1:0.270528,(((A/Shanghai/N13/2007:0.221694,(A/LiaoningTiedong/14/2008:0.77921,A/HeilongjiangQiqiharJianhua/1593/2009:1.8367)1:0.505454)1:0.6104,A/Singapore/215/2008:1.0655)1:0.0847767,A/ShanghaiPudongxin/237/2008:1.24883)1:0.140341,(A/Novosibirsk/1/2008:1.06134,A/Korea/7719/2008:1.87996)1:0.251174)1:0.100076)1:0.0749207,A/RioDeJaneiro/28/2007:0.616191,A/Tumbes/FLA0424/2008:1.36978)1:0.146977)1:0.334074)1:0.455562,A/Canada/101/2006:1.2975)1:0.041077)1:0.0452017,A/Singapore/57/2006:0.901916)1:0.0242044,(A/NewYork/1079/2007:1.01639,A/Japan/63/2007:1.63514)1:0.512744)1:0.0562581)1:1.01825);
\ No newline at end of file
--- a/MTB_data/TB_WGS.fasta_var_cat_merge_miss_0.9_purged_no_can_no_LO_var_cat_merge_fastree
+++ b/MTB_data/TB_WGS.fasta_var_cat_merge_miss_0.9_purged_no_can_no_LO_var_cat_merge_fastree
--- a/MTB_data/TB_WGS.fasta_var_cat_merge_miss_0.9_purged_no_can_no_LO_var_cat_merge_fastree_res_1000_LD
+++ b/MTB_data/TB_WGS.fasta_var_cat_merge_miss_0.9_purged_no_can_no_LO_var_cat_merge_fastree_res_1000_LD
+1	10303
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\ No newline at end of file
--- a/MTB_data/TB_WGS.fasta_var_cat_merge_miss_0.9_purged_no_can_no_LO_var_cat_merge_fastree_res_100_LD
+++ b/MTB_data/TB_WGS.fasta_var_cat_merge_miss_0.9_purged_no_can_no_LO_var_cat_merge_fastree_res_100_LD
+1	10303
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\ No newline at end of file
--- a/MTB_data/TB_WGS.fasta_var_cat_merge_miss_0.9_purged_no_can_no_LO_var_cat_merge_fastree_res_10_LD
+++ b/MTB_data/TB_WGS.fasta_var_cat_merge_miss_0.9_purged_no_can_no_LO_var_cat_merge_fastree_res_10_LD
--- a/MTB_data/TB_WGS.fasta_var_cat_merge_miss_0.9_purged_no_can_no_LO_var_cat_merge_fastree_res_1_LD
+++ b/MTB_data/TB_WGS.fasta_var_cat_merge_miss_0.9_purged_no_can_no_LO_var_cat_merge_fastree_res_1_LD
--- a/MTB_data/TB_WGS.fasta_var_cat_merge_miss_0.9_purged_no_can_no_LO_var_cat_merge_fastree_trimmed_list_RTL_0.95
+++ b/MTB_data/TB_WGS.fasta_var_cat_merge_miss_0.9_purged_no_can_no_LO_var_cat_merge_fastree_trimmed_list_RTL_0.95
--- a/MTB_data/TB_WGS.fasta_var_cat_merge_miss_0.9_purged_no_can_no_LO_var_cat_merge_fastree_trimmed_tree_RTL_0.95
+++ b/MTB_data/TB_WGS.fasta_var_cat_merge_miss_0.9_purged_no_can_no_LO_var_cat_merge_fastree_trimmed_tree_RTL_0.95