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joelnitta/1K_SARS-CoV-2_SG-thorney.xml

Created June 28, 2022 05:41
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XML file for thorney beast run with relaxed clock
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1K_SARS-CoV-2_SG-thorney.xml
<?xml version="1.0" standalone="yes"?>
<!-- Generated by BEAUTi v1.10.4 -->
<!-- by Alexei J. Drummond, Andrew Rambaut and Marc A. Suchard -->
<!-- Department of Computer Science, University of Auckland and -->
<!-- Institute of Evolutionary Biology, University of Edinburgh -->
<!-- David Geffen School of Medicine, University of California, Los Angeles-->
<!-- http://beast.community/ -->
<beast version="1.10.4">
<!-- The list of taxa to be analysed (can also include dates/ages). -->
<!-- ntax=1000 -->
<taxa id="taxa">
<taxon id="Wuhan/WH04/2020|2020-01-05">
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<taxon id="Jiujiang/JX22/2020|2020-01-22">
<date value="2020.0573770491803" direction="forwards" units="years" uncertainty="0.0"/>
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<taxon id="Wuhan/HBCDC-HB-03/2020|2020-01-18">
<date value="2020.0464480874316" direction="forwards" units="years" uncertainty="0.0"/>
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<taxon id="Yunnan/IVDC-YN-003/2020|2020-01-17">
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<taxon id="Nanchang/JX14/2020|2020-01-21">
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<taxon id="Belgium/GHB-03021/2020|2020-02-03">
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<taxon id="Australia/VIC13/2020|2020-01-31">
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<taxon id="Singapore/383/2020|2020-02-15">
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<taxon id="Guangdong/MZ01/2020|2020-02-13">
<date value="2020.1174863387978" direction="forwards" units="years" uncertainty="0.0"/>
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<taxon id="Shandong/LY006-2/2020|2020-01-25">
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<taxon id="England/PHEC-22387/2020|2020-06-03">
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<taxon id="Korea/KCDC2002/2020|2020-01-30">
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<taxon id="South_Korea/KCDC24/2020|2020-02-06">
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<taxon id="India/1-31/2020|2020-01-31">
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<taxon id="Hong_Kong/HKU-907b/2020|2020-01-29">
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<taxon id="Singapore/315/2020|2020-02-19">
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<taxon id="Singapore/188/2020|2020-02-14">
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<taxon id="Uruguay/Mdeo-1/2020|2020-03-13">
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<taxon id="Uruguay/UY-NYUMC864/2020|2020-03-28">
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<taxon id="Uruguay/UY-NYUMC852/2020|2020-03-17">
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<taxon id="South_Korea/KCDC07/2020|2020-01-31">
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<taxon id="South_Korea/KUMC04/2020|2020-02-27">
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<taxon id="South_Korea/KCDC06/2020|2020-01-30">
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<taxon id="Korea/KCDC2018/2020|2020-02-19">
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<taxon id="South_Korea/KCDC03/2020|2020-01-25">
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<taxon id="Korea/KCDC2008/2020|2020-02-05">
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</taxon>
<taxon id="Korea/KCDC2010/2020|2020-02-05">
<date value="2020.0956284153006" direction="forwards" units="years" uncertainty="0.0"/>
</taxon>
<taxon id="Malaysia/MKAK-CL-2020-5096/2020|2020-01-30">
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<taxon id="Malaysia/IMR_WC119/2020|2020-01-30">
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<taxon id="Thailand/SI200468-NT/2020|2020-01-25">
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<taxon id="Thailand/Nonthaburi_193/2020|2020-01-24">
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<taxon id="Thailand/Bangkok_237/2020|2020-01-25">
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<taxon id="Thailand/Bangkok_238/2020|2020-01-31">
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<taxon id="Thailand/SI202620-NT/2020|2020-02-22">
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<taxon id="Thailand/SI202872-NT/2020|2020-02-25">
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<taxon id="Thailand/SI203285-NT/2020|2020-01-23">
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<taxon id="Thailand/Bangkok_1716/2020|2020-02-25">
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<taxon id="Kazakhstan/16173/2020|2020-05-14">
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<taxon id="Kazakhstan/17920/2020|2020-04-15">
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<taxon id="Kazakhstan/22001/2020|2020-04-23">
<date value="2020.308743169399" direction="forwards" units="years" uncertainty="0.0"/>
</taxon>
<taxon id="Kazakhstan/18287/2020|2020-04-16">
<date value="2020.2896174863388" direction="forwards" units="years" uncertainty="0.0"/>
</taxon>
<taxon id="Georgia/Tb-390/2020|2020-03-08">
<date value="2020.1830601092897" direction="forwards" units="years" uncertainty="0.0"/>
</taxon>
<taxon id="Kazakhstan/21927/2020|2020-04-22">
<date value="2020.3060109289618" direction="forwards" units="years" uncertainty="0.0"/>
</taxon>
<taxon id="Spain/COV001605/2020|2020-03-12">
<date value="2020.1939890710382" direction="forwards" units="years" uncertainty="0.0"/>
</taxon>
<taxon id="Spain/COV000665/2020|2020-03-06">
<date value="2020.1775956284152" direction="forwards" units="years" uncertainty="0.0"/>
</taxon>
<taxon id="Australia/VIC595/2020|2020-03-25">
<date value="2020.2295081967213" direction="forwards" units="years" uncertainty="0.0"/>
</taxon>
<taxon id="England/EXET-1375F1/2020|2020-06-03">
<date value="2020.4207650273224" direction="forwards" units="years" uncertainty="0.0"/>
</taxon>
<taxon id="Guangdong/20SF013/2020|2020-01-15">
<date value="2020.0382513661202" direction="forwards" units="years" uncertainty="0.0"/>
</taxon>
<taxon id="Guangdong/20SF012/2020|2020-01-14">
<date value="2020.035519125683" direction="forwards" units="years" uncertainty="0.0"/>
</taxon>
<taxon id="Shenzhen/SZTH-002/2020|2020-01-13">
<date value="2020.032786885246" direction="forwards" units="years" uncertainty="0.0"/>
</taxon>
<taxon id="USA/AZ1/2020|2020-01-22">
<date value="2020.0573770491803" direction="forwards" units="years" uncertainty="0.0"/>
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<taxon id="Shenzhen/HKU-SZ-002/2020|2020-01-10">
<date value="2020.0245901639344" direction="forwards" units="years" uncertainty="0.0"/>
</taxon>
<taxon id="Thailand/SI202205-NT/2020|2020-02-07">
<date value="2020.1010928961748" direction="forwards" units="years" uncertainty="0.0"/>
</taxon>
<taxon id="United_Arab_Emirates/L5630/2020|2020-01-29">
<date value="2020.0765027322404" direction="forwards" units="years" uncertainty="0.0"/>
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<taxon id="Shenzhen/HKU-SZ-005/2020|2020-01-11">
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<taxon id="USA/TX1/2020|2020-02-11">
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<taxon id="Japan/TY-WK-521/2020|2020-01-31">
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<taxon id="Japan/UT-NCGM02/2020|2020-02-01">
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<taxon id="Japan/TY-WK-012/2020|2020-01-29">
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<taxon id="Singapore/4/2020|2020-02-03">
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<taxon id="USA/CA7/2020|2020-02-06">
<date value="2020.0983606557377" direction="forwards" units="years" uncertainty="0.0"/>
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<taxon id="Australia/QLD04/2020|2020-02-05">
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<taxon id="Australia/VIC07/2020|2020-02-08">
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<taxon id="Australia/QLD02/2020|2020-01-30">
<date value="2020.0792349726776" direction="forwards" units="years" uncertainty="0.0"/>
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<taxon id="India/ILSCV13929/2020|2020-05-10">
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<taxon id="Sichuan/SC-PHCC1-026/2020|2020-02-20">
<date value="2020.136612021858" direction="forwards" units="years" uncertainty="0.0"/>
</taxon>
<taxon id="Ghana/2828_S6/2020|2020-03-29">
<date value="2020.24043715847" direction="forwards" units="years" uncertainty="0.0"/>
</taxon>
<taxon id="India/GBRC198/2020|2020-06-08">
<date value="2020.4344262295083" direction="forwards" units="years" uncertainty="0.0"/>
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<taxon id="DRC/04188/2020|2020-04-25">
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<taxon id="Pakistan/NIH-44905/2020|2020-06-02">
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<taxon id="Pakistan/NIH-HAS001/2020|2020-06-02">
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<taxon id="Australia/NSW560/2020|2020-05-24">
<date value="2020.3934426229507" direction="forwards" units="years" uncertainty="0.0"/>
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<taxon id="Nigeria/OS125-CV20/2020|2020-03-29">
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<taxon id="Tunisia/MHT_2/2020|2020-03-24">
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<taxon id="India/GBRC102/2020|2020-04-27">
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<taxon id="Bangladesh/BARJ_CVASU_CTG_506/2020|2020-05-08">
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<taxon id="Bangladesh/BARJ_CVASU_CTG_503/2020|2020-05-13">
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<taxon id="Sichuan/SC-WCH4-287/2020|2020-01-30">
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<taxon id="Malaysia/MKAK-CL-2020-6430/2020|2020-02-04">
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<taxon id="Canada/ON_PHL6884/2020|2020-03-10">
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<taxon id="Taiwan/TSGH-16/2020|2020-03-19">
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<taxon id="Colombia/INS-79489/2020|2020-03-12">
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<taxon id="Vietnam/CM99/2020|2020-02-11">
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<taxon id="Sichuan/IVDC-SC-001/2020|2020-01-15">
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<taxon id="Vietnam/VR03-38142/2020|2020-01-24">
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<taxon id="Korea/KCDC2013/2020|2020-02-23">
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<taxon id="Korea/KCDC2047/2020|2020-02-20">
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<taxon id="Wuhan/WHU01/2020|2020-01-02">
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<taxon id="Hong_Kong/VB20026565-2/2020|2020-02-01">
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<taxon id="Wuhan/IPBCAMS-WH-02/2019|2019-12-30">
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<taxon id="Thailand/61/2020|2020-01-08">
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<taxon id="Korea/KCDC2007/2020|2020-02-05">
<date value="2020.0956284153006" direction="forwards" units="years" uncertainty="0.0"/>
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<taxon id="Wuhan/WIV06/2019|2019-12-30">
<date value="2019.9945205479453" direction="forwards" units="years" uncertainty="0.0"/>
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<taxon id="Japan/DP0059/2020|2020-02-15">
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<taxon id="Hangzhou/ZJU-05/2020|2020-01-22">
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<taxon id="Zhejiang/WZ-02/2020|2020-01-17">
<date value="2020.0437158469945" direction="forwards" units="years" uncertainty="0.0"/>
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<taxon id="Wuhan/WH03/2020|2020-01-01">
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<taxon id="Wuhan/WHU02/2020|2020-01-02">
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<taxon id="Japan/OS-20-07-1/2020|2020-01-23">
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<taxon id="Japan/NA-20-05-1/2020|2020-01-25">
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<taxon id="China/WH-09/2020|2020-01-08">
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<taxon id="Hangzhou/HZCDC0048L/2020|2020-01-21">
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<taxon id="Wuhan/HBCDC-HB-03/2019|2019-12-30">
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<taxon id="Thailand/Nonthaburi_59/2020|2020-01-13">
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8406/2020|2020-04-30:1.3576599999999995E-4,(Russia/Moscow_PMVL-3/2020|2020-05-05:6.788200000000001E-5,Russia/Moscow_PMVL-5/2020|2020-05-05:5.000000000024516E-9):3.393999999999999E-5,(Wales/PHWC-162E01/2020|2020-05-20:6.7888E-5,(Wales/PHWC-162645/2020|2020-05-27:4.999999999970306E-9,Wales/PHWC-16476E/2020|2020-06-10:3.3945999999999976E-5):1.0181100000000005E-4):2.0363800000000002E-4):2.8863999999999973E-5,(Russia/Moscow-67609/2020|2020-03-16:0.0,Hungary/SRC-00055/2020|2020-03-20:0.0,Israel/13075882/2020|2020-03-30:0.0,Switzerland/130020/2020|2020-05-08:3.4161E-5,Japan/Donner27/2020|2020-04-24:6.788399999999999E-5,Argentina/PAIS_A027/2020|2020-04-19:1.7112699999999998E-4,Thailand/Bangkok-0066/2020|2020-03-29:6.937399999999998E-5,Japan/Donner36/2020|2020-05-11:1.0182699999999997E-4,Switzerland/120230/2020|2020-05-01:3.4268000000000005E-5,Canada/ON-UHTC_0074/2020|2020-04-24:6.788200000000001E-5,Morocco/15N/2020|2020-05-15:2.7185800000000004E-4,Germany/BAV-MVP0281/2020|2020-05-07:6.788699999999998E-5,(India/NIV-12019/2020|2020-04-20:6.789600000000002E-5,India/ILSCV15552/2020|2020-05-11:2.0364600000000004E-4):3.3941000000000006E-5,(Japan/Donner32/2020|2020-05-03:3.3951E-5,Japan/Donner6/2020|2020-04-06:3.393500000000002E-5):3.3941000000000006E-5):3.392800000000002E-5,(Bangladesh/BCSIR-NILMRC_064/2020|2020-05-31:6.787999999999998E-5,Bangladesh/BCSIR-NILMRC_076/2020|2020-06-01:0.0,Bangladesh/CHRF_0008/2020|2020-05-16:1.0184099999999998E-4,Bangladesh/icddrb-2083/2020|2020-06-07:1.3577399999999996E-4,Bangladesh/CHRF_0003/2020|2020-04-17:6.796800000000001E-5,Bangladesh/BCSIR-NILMRC_077/2020|2020-06-01:1.01832E-4,Bangladesh/BCSIR-NILMRC_057/2020|2020-05-10:1.35776E-4,Bangladesh/BCSIR-NILMRC_072/2020|2020-05-26:1.35777E-4,Bangladesh/BCSIR-NILMRC_090/2020|2020-06-02:1.0182600000000001E-4,Bangladesh/BCSIR-NILMRC_083/2020|2020-06-01:2.71579E-4,Bangladesh/BCSIR-NILMRC_094/2020|2020-05-23:6.7881E-5,Bangladesh/BCSIR_NILMRC_008/2020|2020-05-21:1.0183000000000002E-4,(Bangladesh/BCSIR-NILMRC_074/2020|2020-06-01:0.0,Bangladesh/BCSIR-NILMRC_075/2020|2020-06-01:0.0):6.788399999999999E-5,(Bangladesh/DU_50758/2020|2020-05-06:3.3941000000000006E-5,Bangladesh/DU_CARS_5586/2020|2020-05-13:4.999999999970306E-9):1.6971899999999992E-4,(Bangladesh/CHRF_0004/2020|2020-04-17:6.795599999999998E-5,Bangladesh/BCSIR-NILMRC_095/2020|2020-05-23:6.788300000000003E-5,Bangladesh/BCSIR-NILMRC_050/2020|2020-05-21:1.35777E-4,(Bangladesh/BCSIR-NILMRC_054/2020|2020-06-01:3.3941000000000006E-5,Bangladesh/BCSIR-NILMRC_051/2020|2020-05-07:5.000000000024516E-9):3.393999999999999E-5):3.3941000000000006E-5):3.3941000000000006E-5,(England/LIVE-A0C95/2020|2020-06-10:2.71553E-4,(England/LCST-24D6B26/2020|2020-06-07:1.0183300000000001E-4,England/BIRM-61331/2020|2020-06-13:1.35772E-4,(England/LIVE-A0318/2020|2020-05-23:0.0,England/LIVE-9FF81/2020|2020-06-08:4.999999999970306E-9):1.35773E-4,(England/BRIS-12DB0B/2020|2020-05-31:6.8074E-5,England/BRIS-12DDD8/2020|2020-06-01:1.9060300000000002E-4):6.230499999999997E-5,(England/CAMB-1B4F94/2020|2020-06-18:4.999999999970306E-9,England/CAMB-1B4F49/2020|2020-06-18:4.999999999970306E-9,England/CAMB-1B4ADF/2020|2020-06-10:3.396400000000004E-5,England/CAMB-1B4FC1/2020|2020-06-18:6.789000000000003E-5,England/CAMB-1B4F1C/2020|2020-06-18:4.999999999970306E-9):2.0371700000000001E-4):3.3937E-5,(Uruguay/UY-NYUMC861/2020|2020-03-25:5.000000000024516E-9,Portugal/PT0608/2020|2020-03-14:3.3923999999999955E-5,Argentina/PAIS_A021/2020|2020-04-11:1.0114900000000003E-4,Chile/Santiago_78/2020|2020-04-04:2.8674000000000017E-5,DRC/1376/2020|2020-04-07:3.452700000000002E-5,England/CAMB-1B3ED4/2020|2020-06-08:1.36417E-4,Poland/Pom6/2020|2020-04-23:1.0211399999999994E-4,England/CAMB-1B5036/2020|2020-06-21:6.788400000000004E-5,(Poland/Pom8/2020|2020-04-27:3.3941000000000006E-5,Poland/Pom9/2020|2020-04-27:4.999999999970306E-9):3.3941000000000006E-5,(England/LCST-24D7008/2020|2020-06-17:4.999999999970306E-9,England/LCST-24D6E0F/2020|2020-06-11:4.999999999970306E-9,England/LCST-24D7141/2020|2020-06-15:4.999999999970306E-9):1.6973399999999994E-4,(England/SHEF-C1399/2020|2020-06-15:0.0,England/SHEF-C8FCB/2020|2020-06-07:0.0,England/SHEF-CD9E6/2020|2020-06-13:3.422899999999999E-5,England/SHEF-CCD18/2020|2020-06-11:4.999999999970306E-9,England/SHEF-D0CE7/2020|2020-06-14:4.999999999970306E-9,England/SHEF-C31D9/2020|2020-06-15:3.422600000000005E-5):6.788200000000001E-5):6.784E-5):6.788300000000003E-5):3.393500000000002E-5):1.4110200000000005E-4):3.393499999999991E-5):3.395800000000006E-5):3.3941000000000006E-5):7.099999999999999E-5):0.0);
</newick>
<constrainedTreeModel id = "treeModel">
<tree idref="startingTree"/>
<constraintsTree>
<tree idref="dataTree"/>
</constraintsTree>
</constrainedTreeModel>
<!-- Statistic for root height of the tree -->
<treeHeightStatistic id="treeModel.rootHeight">
<treeModel idref="treeModel"/>
</treeHeightStatistic>
<!-- Statistic for sum of the branch lengths of the tree (tree length) -->
<treeLengthStatistic id="treeLength">
<treeModel idref="treeModel"/>
</treeLengthStatistic>
<!-- Statistic for time of most recent common ancestor of tree -->
<tmrcaStatistic id="age(root)" absolute="true">
<treeModel idref="treeModel"/>
</tmrcaStatistic>
<!-- Generate a coalescent likelihood -->
<!-- Generate a gmrfSkyGridLikelihood for the Bayesian SkyGrid process -->
<gmrfSkyGridLikelihood id="skygrid">
<populationSizes>
<!-- skygrid.logPopSize is in log units unlike other popSize -->
<parameter id="skygrid.logPopSize" dimension="39" value="1.0"/>
</populationSizes>
<precisionParameter>
<parameter id="skygrid.precision" value="0.1" lower="0.0"/>
</precisionParameter>
<numGridPoints>
<parameter id="skygrid.numGridPoints" value="38.0"/>
</numGridPoints>
<cutOff>
<parameter id="skygrid.cutOff" value="0.7226775956285"/>
</cutOff>
<intervals>
<bigFastTreeIntervals>
<treeModel idref="treeModel"/>
</bigFastTreeIntervals>
</intervals>
</gmrfSkyGridLikelihood>
<thorneyTreeLikelihood id="treeLikelihood">
<constrainedTreeModel idref="treeModel"/>
<!-- The strict clock (Uniform rates across branches) -->
<strictClockBranchRates id="branchRates">
<rate>
<parameter id="clock.rate" value="0.0001" lower="0.0"/>
</rate>
</strictClockBranchRates>
<branchLengthLikelihood id="branchLengthLikelihood" scale="29903.0"/>
<constrainedBranchLengthProvider scale="29903.0" discrete="true" minBranchlength="0.0">
<constrainedTreeModel idref="treeModel"/>
<dataTree>
<tree idref="dataTree"/>
</dataTree>
</constrainedBranchLengthProvider>
</thorneyTreeLikelihood>
<!-- Define operators -->
<operators id="operators" optimizationSchedule="default">
<scaleOperator scaleFactor="0.75" weight="3">
<parameter idref="clock.rate"/>
</scaleOperator>
<nodeHeightOperator type="uniform" weight="500">
<treeModel idref="treeModel"/>
</nodeHeightOperator>
<nodeHeightOperator type="scaleRoot" weight="100" scaleFactor="0.75" >
<treeModel idref="treeModel"/>
</nodeHeightOperator>
<uniformSubtreePruneRegraft weight="500">
<constrainedTreeModel idref="treeModel"/>
</uniformSubtreePruneRegraft>
<narrowExchange weight="100">
<constrainedTreeModel idref="treeModel"/>
</narrowExchange>
<wideExchange weight="100">
<constrainedTreeModel idref="treeModel"/>
</wideExchange>
<wilsonBalding weight="100">
<constrainedTreeModel idref="treeModel"/>
</wilsonBalding>
<gmrfSkygridBlockUpdateOperator scaleFactor="1.1" weight="10">
<gmrfSkygridLikelihood idref="skygrid"/>
</gmrfSkygridBlockUpdateOperator>
<scaleOperator scaleFactor="0.75" weight="1">
<parameter idref="skygrid.precision"/>
</scaleOperator>
<randomWalkOperator windowSize="1.0" weight="1">
<parameter idref="skygrid.logPopSize"/>
</randomWalkOperator>
</operators>
<!-- Define MCMC -->
<mcmc id="mcmc" chainLength="100000000" autoOptimize="true" operatorAnalysis="1K-SARS-CoV-2.ops">
<joint id="joint">
<prior id="prior">
<gammaPrior id="clock.prior" shape="0.001" scale="1000" offset="0.0">
<parameter idref="clock.rate"/>
</gammaPrior>
<gammaPrior id="skygrid.precision.prior" shape="0.001" scale="1000" offset="0.0">
<parameter idref="skygrid.precision"/>
</gammaPrior>
<gmrfSkyGridLikelihood idref="skygrid"/>
</prior>
<likelihood id="likelihood">
<thorneyTreeLikelihood idref="treeLikelihood"/>
</likelihood>
</joint>
<operators idref="operators"/>
<!-- write log to screen -->
<log id="screenLog" logEvery="10000">
<column label="Joint" dp="4" width="12">
<joint idref="joint"/>
</column>
<column label="Prior" dp="4" width="12">
<prior idref="prior"/>
</column>
<column label="Likelihood" dp="4" width="12">
<likelihood idref="likelihood"/>
</column>
<column label="age(root)" sf="6" width="12">
<tmrcaStatistic idref="age(root)"/>
</column>
<column label="clock.rate" sf="6" width="12">
<parameter idref="clock.rate"/>
</column>
</log>
<!-- write log to file -->
<log id="fileLog" logEvery="10000" fileName="1K-SARS-CoV-2.log" overwrite="false">
<joint idref="joint"/>
<prior idref="prior"/>
<likelihood idref="likelihood"/>
<parameter idref="treeModel.rootHeight"/>
<tmrcaStatistic idref="age(root)"/>
<treeLengthStatistic idref="treeLength"/>
<parameter idref="clock.rate"/>
<parameter idref="skygrid.precision"/>
<parameter idref="skygrid.logPopSize"/>
<parameter idref="skygrid.cutOff"/>
<gmrfSkyGridLikelihood idref="skygrid"/>
<treeDataLikelihood idref="treeLikelihood"/>
</log>
<!-- write tree log to file -->
<logTree id="treeFileLog" logEvery="100000" nexusFormat="true" fileName="1K-SARS-CoV-2.trees" sortTranslationTable="true">
<treeModel idref="treeModel"/>
<joint idref="joint"/>
</logTree>
</mcmc>
<report>
<property name="timer">
<mcmc idref="mcmc"/>
</property>
</report>
</beast>
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