Mercurial > repos > iuc > hyphy_strike_ambigs
comparison test-data/summary/nsp8.FADE.json @ 3:204ac950894d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
author | iuc |
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date | Wed, 09 Jun 2021 07:10:18 +0000 |
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2:4bf743518e41 | 3:204ac950894d |
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1 { | |
2 "MLE":{ | |
3 "content":{ | |
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407 }, | |
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609 }, | |
610 "E":{ | |
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1417 }, | |
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1619 }, | |
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1821 }, | |
1822 "L":{ | |
1823 "0": [ | |
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1865 [2.928339977042124, 5.70639772473297, 0.948402634546074, 1.032029571938244], | |
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1867 [1.615962970703708, 4.449484657960352, 0.9442632520867933, 0.9512143221020839], | |
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1876 [2.061939370468227, 5.420863800335724, 0.9465538070312275, 0.9943870241394031], | |
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1888 [3.961403235394677, 5.422023468184566, 0.946800063314746, 0.9992498234603361], | |
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1900 [2.133616121408357, 5.420859739072831, 0.9465675006916835, 0.9946562546086741], | |
1901 [1.497164287699758, 5.422627502948917, 0.9464301702299115, 0.9919624378984979], | |
1902 [2.333746133560598, 5.419559847919818, 0.9465987007191887, 0.9952701927027651], | |
1903 [1.18951597460728, 3.916974679298278, 0.9428722673557071, 0.9266864051379886], | |
1904 [2.061939370468227, 5.420863800335724, 0.9465538070312277, 0.9943870241394073], | |
1905 [2.333746133560598, 5.419559847919818, 0.9465987007191887, 0.9952701927027651], | |
1906 [1.615962970703708, 4.449484657960352, 0.9442632520867933, 0.9512143221020839], | |
1907 [1.168458523168688, 5.424121714948564, 0.9463208537472177, 0.9898279843848133], | |
1908 [1.131030942404497, 5.42527464930169, 0.9463117766883116, 0.9896511415618324], | |
1909 [2.061939370468227, 5.420863800335724, 0.9465538070312275, 0.9943870241394031], | |
1910 [1.816676323044878, 5.420955334666949, 0.9465105338550853, 0.9935371381867882], | |
1911 [3.961403235394676, 5.422023468184567, 0.946800063314746, 0.9992498234603361], | |
1912 [1.168458523168687, 5.424121714948565, 0.946320853747218, 0.9898279843848176], | |
1913 [1.816676323044878, 5.420955334666949, 0.9465105338550853, 0.9935371381867882], | |
1914 [2.928339977042124, 5.70639772473297, 0.948402634546074, 1.032029571938244], | |
1915 [1.049153359135308, 2.901454954464303, 0.9398509650181786, 0.8773184143424232], | |
1916 [1.168458523168688, 5.424121714948564, 0.9463208537472177, 0.9898279843848133], | |
1917 [1.816676323044878, 5.420955334666949, 0.9465105338550853, 0.9935371381867882], | |
1918 [2.928339977042124, 5.70639772473297, 0.948402634546074, 1.032029571938244], | |
1919 [1.189515974607279, 3.916974679298278, 0.9428722673557068, 0.9266864051379847], | |
1920 [2.333746133560598, 5.419559847919818, 0.9465987007191887, 0.9952701927027651], | |
1921 [2.928339977042124, 5.70639772473297, 0.948402634546074, 1.032029571938244], | |
1922 [1.497164287699758, 5.422627502948917, 0.9464301702299115, 0.9919624378984979], | |
1923 [1.93762925955464, 5.421125094492752, 0.9465333225842832, 0.9939845377595354], | |
1924 [1.497164287699758, 5.422627502948917, 0.9464301702299115, 0.9919624378984979], | |
1925 [2.061939370468227, 5.420863800335724, 0.9465538070312275, 0.9943870241394031], | |
1926 [2.928339977042124, 5.70639772473297, 0.948402634546074, 1.032029571938244], | |
1927 [1.93762925955464, 5.421125094492752, 0.9465333225842832, 0.9939845377595354], | |
1928 [1.93762925955464, 5.421125094492752, 0.9465333225842832, 0.9939845377595354], | |
1929 [1.065275359077655, 5.077115826582193, 0.945595828166146, 0.975888636920944], | |
1930 [1.065275359077655, 5.077115826582193, 0.945595828166146, 0.975888636920944], | |
1931 [1.93762925955464, 5.421125094492752, 0.9465333225842832, 0.9939845377595354], | |
1932 [1.93762925955464, 5.421125094492752, 0.9465333225842832, 0.9939845377595354], | |
1933 [2.061939370468227, 5.420863800335724, 0.9465538070312275, 0.9943870241394031], | |
1934 [1.18951597460728, 3.916974679298278, 0.9428722673557071, 0.9266864051379886], | |
1935 [1.497164287699758, 5.422627502948917, 0.9464301702299115, 0.9919624378984979], | |
1936 [4.156291360648809, 5.421653451555605, 0.9468378509926452, 1.000000000000016], | |
1937 [0.8524234737980562, 5.429506339413134, 0.9461359334265204, 0.9862370553947043], | |
1938 [1.615962970703708, 4.449484657960352, 0.9442632520867933, 0.9512143221020839], | |
1939 [2.518860792832839, 5.420488467412673, 0.9466310469336244, 0.9959074427429486], | |
1940 [2.928339977042124, 5.70639772473297, 0.948402634546074, 1.032029571938244], | |
1941 [1.93762925955464, 5.421125094492752, 0.9465333225842832, 0.9939845377595354], | |
1942 [1.065275359077655, 5.077115826582193, 0.945595828166146, 0.975888636920944], | |
1943 [1.065275359077655, 5.077115826582193, 0.945595828166146, 0.975888636920944], | |
1944 [2.518860792832839, 5.420488467412673, 0.9466310469336244, 0.9959074427429486], | |
1945 [2.928339977042124, 5.70639772473297, 0.948402634546074, 1.032029571938244], | |
1946 [8.605319397024729, 5.148442936590988, 0.9489291929620119, 1.043249064830302], | |
1947 [1.168458523168688, 5.424121714948564, 0.9463208537472177, 0.9898279843848133], | |
1948 [2.061939370468227, 5.420863800335723, 0.9465538070312278, 0.9943870241394095], | |
1949 [2.061939370468227, 5.420863800335723, 0.9465538070312278, 0.9943870241394095], | |
1950 [2.333746133560598, 5.419559847919818, 0.9465987007191887, 0.9952701927027651], | |
1951 [2.928339977042124, 5.70639772473297, 0.948402634546074, 1.032029571938244], | |
1952 [1.816676323044878, 5.420955334666949, 0.9465105338550853, 0.9935371381867882], | |
1953 [1.615962970703708, 4.449484657960352, 0.9442632520867933, 0.9512143221020839], | |
1954 [1.615962970703708, 4.449484657960352, 0.9442632520867933, 0.9512143221020839], | |
1955 [1.065275359077655, 5.077115826582193, 0.945595828166146, 0.975888636920944], | |
1956 [20.89968712278805, 5.409915565392185, 0.9494914323826832, 1.055487064480197], | |
1957 [1.497164287699758, 5.422627502948916, 0.9464301702299114, 0.9919624378984957], | |
1958 [1.494623348852311, 5.422623562879634, 0.9464334674889038, 0.992026953712027], | |
1959 [1.93762925955464, 5.421125094492752, 0.9465333225842832, 0.9939845377595354], | |
1960 [1.168458523168688, 5.424121714948564, 0.9463208537472177, 0.9898279843848133], | |
1961 [1.494623348852311, 5.422623562879634, 0.9464334674889038, 0.992026953712027], | |
1962 [2.333746133560598, 5.419559847919818, 0.9465987007191887, 0.9952701927027651], | |
1963 [1.93762925955464, 5.421125094492752, 0.9465333225842832, 0.9939845377595354], | |
1964 [1.168458523168688, 5.424121714948564, 0.9463208537472177, 0.9898279843848133], | |
1965 [0.8524234737980562, 5.429506339413134, 0.9461359334265204, 0.9862370553947043], | |
1966 [1.497164287699758, 5.422627502948917, 0.9464301702299115, 0.9919624378984979], | |
1967 [4.156291360648809, 5.421653451555605, 0.9468378509926452, 1.000000000000016], | |
1968 [1.168458523168688, 5.424121714948564, 0.946320853747218, 0.9898279843848176], | |
1969 [8.605318423907464, 5.148442396905879, 0.94892919194625, 1.043249042964098], | |
1970 [1.049153359135308, 2.901454954464303, 0.9398509650181786, 0.8773184143424232], | |
1971 [1.168458523168688, 5.424121714948564, 0.946320853747218, 0.9898279843848176], | |
1972 [1.494623348852311, 5.422623562879634, 0.9464334674889038, 0.992026953712027], | |
1973 [2.061939370468227, 5.420863800335724, 0.9465538070312275, 0.9943870241394031], | |
1974 [1.131030942404497, 5.425274649301689, 0.9463117766883112, 0.989651141561826], | |
1975 [2.061939370468227, 5.420863800335724, 0.9465538070312275, 0.9943870241394031], | |
1976 [2.928339977042124, 5.70639772473297, 0.948402634546074, 1.032029571938244], | |
1977 [4.156291360648809, 5.421653451555605, 0.9468378509926452, 1.000000000000016], | |
1978 [2.133616121408357, 5.420859739072831, 0.9465675006916835, 0.9946562546086741], | |
1979 [1.065275359077655, 5.077115826582193, 0.945595828166146, 0.975888636920944], | |
1980 [3.961403235394677, 5.422023468184566, 0.946800063314746, 0.9992498234603361], | |
1981 [3.961403235394677, 5.422023468184566, 0.946800063314746, 0.9992498234603361], | |
1982 [1.615962970703708, 4.449484657960352, 0.9442632520867933, 0.9512143221020839], | |
1983 [1.615962970703708, 4.449484657960352, 0.9442632520867933, 0.9512143221020839], | |
1984 [1.497164287699758, 5.422627502948916, 0.9464301702299114, 0.9919624378984957], | |
1985 [2.061939370468227, 5.420863800335724, 0.9465538070312275, 0.9943870241394031], | |
1986 [1.497164287699758, 5.422627502948916, 0.9464301702299114, 0.9919624378984957], | |
1987 [1.131030942404497, 5.425274649301688, 0.9463117766883116, 0.9896511415618324], | |
1988 [2.333746133560598, 5.419559847919818, 0.9465987007191887, 0.9952701927027651], | |
1989 [1.065275359077655, 5.077115826582193, 0.945595828166146, 0.975888636920944], | |
1990 [1.615962970703708, 4.449484657960352, 0.9442632520867933, 0.9512143221020839], | |
1991 [3.961403235394677, 5.422023468184566, 0.946800063314746, 0.9992498234603361], | |
1992 [2.928339977042124, 5.70639772473297, 0.948402634546074, 1.032029571938244], | |
1993 [1.131030942404497, 5.425274649301689, 0.9463117766883113, 0.9896511415618282], | |
1994 [2.133616121408357, 5.420859739072831, 0.9465675006916835, 0.9946562546086741], | |
1995 [1.065275359077655, 5.077115826582193, 0.945595828166146, 0.975888636920944], | |
1996 [1.131030942404497, 5.425274649301689, 0.9463117766883112, 0.989651141561826], | |
1997 [1.816676323044878, 5.420955334666949, 0.9465105338550853, 0.9935371381867882], | |
1998 [1.497164287699758, 5.422627502948917, 0.9464301702299115, 0.9919624378984979], | |
1999 [1.93762925955464, 5.421125094492752, 0.9465333225842832, 0.9939845377595354], | |
2000 [1.131030942404497, 5.425274649301689, 0.9463117766883112, 0.989651141561826], | |
2001 [2.518860792832839, 5.420488467412673, 0.9466310469336244, 0.9959074427429486], | |
2002 [1.93762925955464, 5.421125094492752, 0.9465333225842832, 0.9939845377595354], | |
2003 [2.928339977042124, 5.70639772473297, 0.948402634546074, 1.032029571938244], | |
2004 [2.061939370468227, 5.420863800335724, 0.9465538070312275, 0.9943870241394031], | |
2005 [4.156291360648809, 5.421653451555605, 0.9468378509926452, 1.000000000000016], | |
2006 [2.518860792832839, 5.420488467412673, 0.9466310469336244, 0.9959074427429486], | |
2007 [2.928339977042124, 5.70639772473297, 0.948402634546074, 1.032029571938244], | |
2008 [1.065275359077655, 5.077115826582193, 0.945595828166146, 0.975888636920944], | |
2009 [1.615962970703708, 4.449484657960352, 0.9442632520867933, 0.9512143221020839], | |
2010 [1.168458523168688, 5.424121714948564, 0.9463208537472176, 0.9898279843848112], | |
2011 [2.061939370468227, 5.420863800335724, 0.9465538070312275, 0.9943870241394031], | |
2012 [2.928339977042124, 5.70639772473297, 0.948402634546074, 1.032029571938244], | |
2013 [1.18951597460728, 3.916974679298277, 0.942872267355707, 0.9266864051379866], | |
2014 [2.061939370468227, 5.420863800335724, 0.9465538070312275, 0.9943870241394031], | |
2015 [1.93762925955464, 5.421125094492752, 0.9465333225842832, 0.9939845377595354], | |
2016 [1.131030942404497, 5.425274649301689, 0.9463117766883112, 0.989651141561826], | |
2017 [2.061939370468227, 5.420863800335724, 0.9465538070312275, 0.9943870241394031], | |
2018 [1.615962970703708, 4.449484657960352, 0.9442632520867933, 0.9512143221020839], | |
2019 [2.333746133560598, 5.419559847919818, 0.9465987007191887, 0.9952701927027651], | |
2020 [2.928339977042124, 5.70639772473297, 0.948402634546074, 1.032029571938244], | |
2021 [17.66001793829528, 5.39639482035181, 0.9494503072651478, 1.0545826854226] | |
2022 ] | |
2023 }, | |
2024 "M":{ | |
2025 "0": [ | |
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3235 }, | |
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4041 [17.58047881587558, 5.533472866110234, 0.9497915250859426, 1.057326684928253] | |
4042 ] | |
4043 } | |
4044 }, | |
4045 "headers": [ | |
4046 ["rate", "Mean posterior relative rate at a site"], | |
4047 ["bias", "Mean posterior bias parameter at a site"], | |
4048 ["Prob[bias>0]", "Posterior probability of substitution bias"], | |
4049 ["BayesFactor[bias>0]", "Empiricial Bayes Factor for substitution bias"] | |
4050 ] | |
4051 }, | |
4052 "analysis":{ | |
4053 "authors":"Sergei L Kosakovsky Pond", | |
4054 "citation":"TBD", | |
4055 "contact":"spond@temple.edu", | |
4056 "info":"FADE (FUBAR Approach to Directional Evolution) is a fast method to test whether or not a subset of sites in a protein alignment\n evolve towards a particular residue along a subset of branches at accelerated rates compared to reference model.\n FADE uses a random effects model and latent Dirichlet allocation (LDA) - inspired approximation methods to allocate sites to rate classes.", | |
4057 "requirements":"A protein alignment and a **rooted** phylogenetic tree (optionally annotated with {})", | |
4058 "version":"0.2" | |
4059 }, | |
4060 "branch attributes":{ | |
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4295 [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197] | |
4296 ], | |
4297 "name":"fade.filter.default" | |
4298 } | |
4299 }, | |
4300 "fits":{ | |
4301 "GTR":{ | |
4302 "AIC-c":2132.976178408104, | |
4303 "Equilibrium frequencies": [ | |
4304 [0.1248208897908482], | |
4305 [0.01617036526614388], | |
4306 [0.0613808518960904], | |
4307 [0.04055833016590132], | |
4308 [0.02361019337992023], | |
4309 [0.01515291048942647], | |
4310 [0.003618367567326987], | |
4311 [0.06696619468919553], | |
4312 [0.07318247552353704], | |
4313 [0.09484732957068891], | |
4314 [0.04357587031582835], | |
4315 [0.07063215442635443], | |
4316 [0.02791277924451734], | |
4317 [0.05238618781636656], | |
4318 [0.0283595326742204], | |
4319 [0.07858180163722514], | |
4320 [0.06066736366044741], | |
4321 [0.07017285888042277], | |
4322 [0.01010447921662212], | |
4323 [0.03729906378891648] | |
4324 ], | |
4325 "Log Likelihood":-784.4237858240024, | |
4326 "Rate Distributions":null, | |
4327 "display order":0, | |
4328 "estimated parameters":270 | |
4329 } | |
4330 }, | |
4331 "input":{ | |
4332 "file name":"/home/aglucaci/SARS-CoV-2/clades/B-1-617/nsp8.aa.fas", | |
4333 "number of sequences":32, | |
4334 "number of sites":198, | |
4335 "partition count":1, | |
4336 "trees":{ | |
4337 "0":"(((((EPI_ISL_1615709_HCOV_19_ENGLAND_CAMC_14E792B_2021,GB_MW523870_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_LA_CDC_STM_A100279_2021_SEGMENT_NULL_HOST_HUMAN)Node4,EPI_ISL_1592421_HCOV_19_USA_MA_CDC_STM_000044850_2021)Node3,(EPI_ISL_1652118_HCOV_19_SINGAPORE_575_2021,(EPI_ISL_1652105_HCOV_19_SINGAPORE_561_2021,((GB_MW593074_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_MN_MDH_2645_2021_SEGMENT_NULL_HOST_HUMAN,GB_MW154124_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_AUS_VIC7567_2020_SEGMENT_NULL_HOST_HUMAN)Node13,(EPI_ISL_1416968_HCOV_19_GUADELOUPE_IPP06229_2021,EPI_ISL_1544068_HCOV_19_INDIA_MH_NCCS_RT231527_2021)Node16)Node12)Node10)Node8)Node2,((GB_MT226610_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_CHN_KMS1_2020_SEGMENT_NULL_HOST_HUMAN,EPI_ISL_1589870_HCOV_19_INDIA_WB_1931501009078_2021)Node20,((GB_MT326179_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_WA_UW_1572_2020_SEGMENT_NULL_HOST_HUMAN,EPI_ISL_1589885_HCOV_19_INDIA_WB_1931300250528_2021)Node24,((((GB_MW345265_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_MD_MDH_0448_2020_SEGMENT_NULL_HOST_HUMAN,GB_MW525063_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_MI_CDC_STM_0000013_D10_2021_SEGMENT_NULL_HOST_HUMAN)Node30,((((GB_MW585851_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_GA_CDC_STM_000004152_2021_SEGMENT_NULL_HOST_HUMAN,(GB_MW583322_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_AL_CDC_STM_000001665_2021_SEGMENT_NULL_HOST_HUMAN,(GB_MW562702_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_UT_UPHL_2102128070_2020_SEGMENT_NULL_HOST_HUMAN,EPI_ISL_1384851_HCOV_19_INDIA_MH_NCCS_ND13683_2021)Node40)Node38)Node36,((EPI_ISL_1357692_HCOV_19_INDIA_WB_1931500870015_2021,GB_MW486334_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_WI_UW_2535_2020_SEGMENT_NULL_HOST_HUMAN)Node44,(EPI_ISL_1533793_HCOV_19_INDIA_MH_NCCS_CHN21027888_2021,GB_LR757997_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_UNKNOWN_LR757997_SEGMENT_NULL_HOST_HUMAN)Node47)Node43)Node35,(EPI_ISL_1415270_HCOV_19_INDIA_MH_NCCS_BJ2_2021,EPI_ISL_1543980_HCOV_19_SINGAPORE_490_2021)Node50)Node34,EPI_ISL_1181694_HCOV_19_USA_DE_DHSS_B1064373_2021)Node33)Node29,(EPI_ISL_1632256_HCOV_19_ENGLAND_RAND_14E1D70_2021,GB_MT745751_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_BGD_DNAS_ISL_BRB_2020_SEGMENT_NULL_HOST_HUMAN)Node54)Node28,((GB_MW585867_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_CA_CDC_STM_000003621_2021_SEGMENT_NULL_HOST_HUMAN,GB_MW540189_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_MA_MASPHL_01215_2020_SEGMENT_NULL_HOST_HUMAN)Node58,EPI_ISL_1573247_HCOV_19_GERMANY_UN_RKI_I_068985_2021)Node57)Node27)Node23)Node19)Node1,REFERENCE)" | |
4338 } | |
4339 }, | |
4340 "settings":{ | |
4341 "bayes factor":100, | |
4342 "burn-in":1000000, | |
4343 "chain-length":2000000, | |
4344 "chains":1, | |
4345 "concentration":0.5, | |
4346 "grid size":20, | |
4347 "method":"Variational-Bayes", | |
4348 "samples":100 | |
4349 }, | |
4350 "site annotations":{ | |
4351 "headers":{ | |
4352 "Composition":"Amino acid composition of site", | |
4353 "Substitutions":"Substitution history on selected branches" | |
4354 }, | |
4355 "site annotations":{ | |
4356 "0": [ | |
4357 ["A40", ""], | |
4358 ["I40", ""], | |
4359 ["A40", ""], | |
4360 ["S40", ""], | |
4361 ["D1,E39", "E->D(1)"], | |
4362 ["F40", ""], | |
4363 ["S40", ""], | |
4364 ["S40", ""], | |
4365 ["F1,L39", "L->F(1)"], | |
4366 ["P40", ""], | |
4367 ["S40", ""], | |
4368 ["Y40", ""], | |
4369 ["A40", ""], | |
4370 ["A40", ""], | |
4371 ["F40", ""], | |
4372 ["A40", ""], | |
4373 ["T40", ""], | |
4374 ["A40", ""], | |
4375 ["Q40", ""], | |
4376 ["E40", ""], | |
4377 ["A39,V1", "A->V(1)"], | |
4378 ["Y40", ""], | |
4379 ["E40", ""], | |
4380 ["Q40", ""], | |
4381 ["A40", ""], | |
4382 ["V40", ""], | |
4383 ["A40", ""], | |
4384 ["N40", ""], | |
4385 ["G40", ""], | |
4386 ["D40", ""], | |
4387 ["S40", ""], | |
4388 ["E40", ""], | |
4389 ["V40", ""], | |
4390 ["V40", ""], | |
4391 ["L40", ""], | |
4392 ["K40", ""], | |
4393 ["K38,N2", "K->N(1)"], | |
4394 ["L40", ""], | |
4395 ["K40", ""], | |
4396 ["K40", ""], | |
4397 ["S40", ""], | |
4398 ["L40", ""], | |
4399 ["N40", ""], | |
4400 ["V40", ""], | |
4401 ["A40", ""], | |
4402 ["K40", ""], | |
4403 ["S40", ""], | |
4404 ["E40", ""], | |
4405 ["F40", ""], | |
4406 ["D40", ""], | |
4407 ["R40", ""], | |
4408 ["D40", ""], | |
4409 ["A40", ""], | |
4410 ["A40", ""], | |
4411 ["M40", ""], | |
4412 ["Q40", ""], | |
4413 ["R40", ""], | |
4414 ["K40", ""], | |
4415 ["L40", ""], | |
4416 ["E40", ""], | |
4417 ["K40", ""], | |
4418 ["M40", ""], | |
4419 ["A40", ""], | |
4420 ["D40", ""], | |
4421 ["Q40", ""], | |
4422 ["A40", ""], | |
4423 ["M39,V1", "M->V(1)"], | |
4424 ["T40", ""], | |
4425 ["Q40", ""], | |
4426 ["M40", ""], | |
4427 ["Y40", ""], | |
4428 ["K40", ""], | |
4429 ["Q40", ""], | |
4430 ["A40", ""], | |
4431 ["R40", ""], | |
4432 ["S40", ""], | |
4433 ["E40", ""], | |
4434 ["D40", ""], | |
4435 ["K40", ""], | |
4436 ["R40", ""], | |
4437 ["A40", ""], | |
4438 ["K40", ""], | |
4439 ["V40", ""], | |
4440 ["T40", ""], | |
4441 ["S40", ""], | |
4442 ["A40", ""], | |
4443 ["M40", ""], | |
4444 ["Q40", ""], | |
4445 ["T40", ""], | |
4446 ["M40", ""], | |
4447 ["L40", ""], | |
4448 ["F40", ""], | |
4449 ["T40", ""], | |
4450 ["M40", ""], | |
4451 ["L40", ""], | |
4452 ["R40", ""], | |
4453 ["K40", ""], | |
4454 ["L40", ""], | |
4455 ["D40", ""], | |
4456 ["N40", ""], | |
4457 ["D40", ""], | |
4458 ["A40", ""], | |
4459 ["L40", ""], | |
4460 ["N40", ""], | |
4461 ["N40", ""], | |
4462 ["I40", ""], | |
4463 ["I40", ""], | |
4464 ["N40", ""], | |
4465 ["N40", ""], | |
4466 ["A40", ""], | |
4467 ["R40", ""], | |
4468 ["D40", ""], | |
4469 ["G40", ""], | |
4470 ["C40", ""], | |
4471 ["V40", ""], | |
4472 ["P40", ""], | |
4473 ["L40", ""], | |
4474 ["N40", ""], | |
4475 ["I40", ""], | |
4476 ["I40", ""], | |
4477 ["P40", ""], | |
4478 ["L40", ""], | |
4479 ["I1,T39", "T->I(1)"], | |
4480 ["T40", ""], | |
4481 ["A40", ""], | |
4482 ["A40", ""], | |
4483 ["K40", ""], | |
4484 ["L40", ""], | |
4485 ["M40", ""], | |
4486 ["V40", ""], | |
4487 ["V40", ""], | |
4488 ["I40", ""], | |
4489 ["P38,S2", "P->S(1)"], | |
4490 ["D40", ""], | |
4491 ["Y40", ""], | |
4492 ["N40", ""], | |
4493 ["T40", ""], | |
4494 ["Y40", ""], | |
4495 ["K40", ""], | |
4496 ["N40", ""], | |
4497 ["T40", ""], | |
4498 ["C40", ""], | |
4499 ["D40", ""], | |
4500 ["G40", ""], | |
4501 ["T40", ""], | |
4502 ["I1,T39", "T->I(1)"], | |
4503 ["F40", ""], | |
4504 ["T40", ""], | |
4505 ["Y40", ""], | |
4506 ["A40", ""], | |
4507 ["S40", ""], | |
4508 ["A40", ""], | |
4509 ["L40", ""], | |
4510 ["W40", ""], | |
4511 ["E40", ""], | |
4512 ["I40", ""], | |
4513 ["Q40", ""], | |
4514 ["Q40", ""], | |
4515 ["V40", ""], | |
4516 ["V40", ""], | |
4517 ["D40", ""], | |
4518 ["A40", ""], | |
4519 ["D40", ""], | |
4520 ["S40", ""], | |
4521 ["K40", ""], | |
4522 ["I40", ""], | |
4523 ["V40", ""], | |
4524 ["Q40", ""], | |
4525 ["L40", ""], | |
4526 ["S40", ""], | |
4527 ["E40", ""], | |
4528 ["I40", ""], | |
4529 ["S40", ""], | |
4530 ["M40", ""], | |
4531 ["D40", ""], | |
4532 ["N40", ""], | |
4533 ["S40", ""], | |
4534 ["P40", ""], | |
4535 ["N40", ""], | |
4536 ["L40", ""], | |
4537 ["A40", ""], | |
4538 ["W40", ""], | |
4539 ["P40", ""], | |
4540 ["L40", ""], | |
4541 ["I40", ""], | |
4542 ["V40", ""], | |
4543 ["T40", ""], | |
4544 ["A40", ""], | |
4545 ["L40", ""], | |
4546 ["R40", ""], | |
4547 ["A40", ""], | |
4548 ["N40", ""], | |
4549 ["S40", ""], | |
4550 ["A40", ""], | |
4551 ["V40", ""], | |
4552 ["K40", ""], | |
4553 ["L40", ""], | |
4554 ["H1,Q39", "Q->H(1)"] | |
4555 ] | |
4556 } | |
4557 }, | |
4558 "tested":{ | |
4559 "0":{ | |
4560 "EPI_ISL_1181694_HCOV_19_USA_DE_DHSS_B1064373_2021":"test", | |
4561 "EPI_ISL_1357692_HCOV_19_INDIA_WB_1931500870015_2021":"test", | |
4562 "EPI_ISL_1384851_HCOV_19_INDIA_MH_NCCS_ND13683_2021":"test", | |
4563 "EPI_ISL_1415270_HCOV_19_INDIA_MH_NCCS_BJ2_2021":"test", | |
4564 "EPI_ISL_1416968_HCOV_19_GUADELOUPE_IPP06229_2021":"test", | |
4565 "EPI_ISL_1533793_HCOV_19_INDIA_MH_NCCS_CHN21027888_2021":"test", | |
4566 "EPI_ISL_1543980_HCOV_19_SINGAPORE_490_2021":"test", | |
4567 "EPI_ISL_1544068_HCOV_19_INDIA_MH_NCCS_RT231527_2021":"test", | |
4568 "EPI_ISL_1573247_HCOV_19_GERMANY_UN_RKI_I_068985_2021":"test", | |
4569 "EPI_ISL_1589870_HCOV_19_INDIA_WB_1931501009078_2021":"test", | |
4570 "EPI_ISL_1589885_HCOV_19_INDIA_WB_1931300250528_2021":"test", | |
4571 "EPI_ISL_1592421_HCOV_19_USA_MA_CDC_STM_000044850_2021":"test", | |
4572 "EPI_ISL_1615709_HCOV_19_ENGLAND_CAMC_14E792B_2021":"test", | |
4573 "EPI_ISL_1632256_HCOV_19_ENGLAND_RAND_14E1D70_2021":"test", | |
4574 "EPI_ISL_1652105_HCOV_19_SINGAPORE_561_2021":"test", | |
4575 "EPI_ISL_1652118_HCOV_19_SINGAPORE_575_2021":"test", | |
4576 "GB_LR757997_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_UNKNOWN_LR757997_SEGMENT_NULL_HOST_HUMAN":"background", | |
4577 "GB_MT226610_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_CHN_KMS1_2020_SEGMENT_NULL_HOST_HUMAN":"background", | |
4578 "GB_MT326179_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_WA_UW_1572_2020_SEGMENT_NULL_HOST_HUMAN":"background", | |
4579 "GB_MT745751_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_BGD_DNAS_ISL_BRB_2020_SEGMENT_NULL_HOST_HUMAN":"background", | |
4580 "GB_MW154124_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_AUS_VIC7567_2020_SEGMENT_NULL_HOST_HUMAN":"background", | |
4581 "GB_MW345265_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_MD_MDH_0448_2020_SEGMENT_NULL_HOST_HUMAN":"background", | |
4582 "GB_MW486334_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_WI_UW_2535_2020_SEGMENT_NULL_HOST_HUMAN":"background", | |
4583 "GB_MW523870_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_LA_CDC_STM_A100279_2021_SEGMENT_NULL_HOST_HUMAN":"background", | |
4584 "GB_MW525063_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_MI_CDC_STM_0000013_D10_2021_SEGMENT_NULL_HOST_HUMAN":"background", | |
4585 "GB_MW540189_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_MA_MASPHL_01215_2020_SEGMENT_NULL_HOST_HUMAN":"background", | |
4586 "GB_MW562702_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_UT_UPHL_2102128070_2020_SEGMENT_NULL_HOST_HUMAN":"background", | |
4587 "GB_MW583322_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_AL_CDC_STM_000001665_2021_SEGMENT_NULL_HOST_HUMAN":"background", | |
4588 "GB_MW585851_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_GA_CDC_STM_000004152_2021_SEGMENT_NULL_HOST_HUMAN":"background", | |
4589 "GB_MW585867_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_CA_CDC_STM_000003621_2021_SEGMENT_NULL_HOST_HUMAN":"background", | |
4590 "GB_MW593074_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_MN_MDH_2645_2021_SEGMENT_NULL_HOST_HUMAN":"background", | |
4591 "Node1":"test", | |
4592 "Node10":"test", | |
4593 "Node12":"test", | |
4594 "Node13":"background", | |
4595 "Node16":"test", | |
4596 "Node19":"test", | |
4597 "Node2":"test", | |
4598 "Node20":"test", | |
4599 "Node23":"test", | |
4600 "Node24":"test", | |
4601 "Node27":"test", | |
4602 "Node28":"test", | |
4603 "Node29":"test", | |
4604 "Node3":"test", | |
4605 "Node30":"background", | |
4606 "Node33":"test", | |
4607 "Node34":"test", | |
4608 "Node35":"test", | |
4609 "Node36":"background", | |
4610 "Node38":"background", | |
4611 "Node4":"test", | |
4612 "Node40":"background", | |
4613 "Node43":"test", | |
4614 "Node44":"test", | |
4615 "Node47":"test", | |
4616 "Node50":"test", | |
4617 "Node54":"test", | |
4618 "Node57":"test", | |
4619 "Node58":"background", | |
4620 "Node8":"test", | |
4621 "REFERENCE":"background" | |
4622 } | |
4623 }, | |
4624 "timers":{ | |
4625 "Baseline Fit":{ | |
4626 "order":1, | |
4627 "timer":202 | |
4628 }, | |
4629 "Overall":{ | |
4630 "order":0, | |
4631 "timer":244 | |
4632 }, | |
4633 "Residue A analysis":{ | |
4634 "order":21, | |
4635 "timer":2 | |
4636 }, | |
4637 "Residue C analysis":{ | |
4638 "order":21, | |
4639 "timer":2 | |
4640 }, | |
4641 "Residue D analysis":{ | |
4642 "order":21, | |
4643 "timer":2 | |
4644 }, | |
4645 "Residue E analysis":{ | |
4646 "order":21, | |
4647 "timer":2 | |
4648 }, | |
4649 "Residue F analysis":{ | |
4650 "order":21, | |
4651 "timer":2 | |
4652 }, | |
4653 "Residue G analysis":{ | |
4654 "order":21, | |
4655 "timer":2 | |
4656 }, | |
4657 "Residue H analysis":{ | |
4658 "order":21, | |
4659 "timer":2 | |
4660 }, | |
4661 "Residue I analysis":{ | |
4662 "order":21, | |
4663 "timer":2 | |
4664 }, | |
4665 "Residue K analysis":{ | |
4666 "order":21, | |
4667 "timer":2 | |
4668 }, | |
4669 "Residue L analysis":{ | |
4670 "order":21, | |
4671 "timer":2 | |
4672 }, | |
4673 "Residue M analysis":{ | |
4674 "order":21, | |
4675 "timer":2 | |
4676 }, | |
4677 "Residue N analysis":{ | |
4678 "order":21, | |
4679 "timer":2 | |
4680 }, | |
4681 "Residue P analysis":{ | |
4682 "order":21, | |
4683 "timer":2 | |
4684 }, | |
4685 "Residue Q analysis":{ | |
4686 "order":21, | |
4687 "timer":2 | |
4688 }, | |
4689 "Residue R analysis":{ | |
4690 "order":21, | |
4691 "timer":3 | |
4692 }, | |
4693 "Residue S analysis":{ | |
4694 "order":21, | |
4695 "timer":2 | |
4696 }, | |
4697 "Residue T analysis":{ | |
4698 "order":21, | |
4699 "timer":2 | |
4700 }, | |
4701 "Residue V analysis":{ | |
4702 "order":21, | |
4703 "timer":2 | |
4704 }, | |
4705 "Residue W analysis":{ | |
4706 "order":21, | |
4707 "timer":3 | |
4708 }, | |
4709 "Residue Y analysis":{ | |
4710 "order":21, | |
4711 "timer":2 | |
4712 } | |
4713 } | |
4714 } |