Mercurial > repos > iuc > hyphy_bgm
comparison test-data/summary/ORF6.FADE.json @ 27:1c3a2f66373f 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 07:09:31 +0000 |
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26:d1c977aee228 | 27:1c3a2f66373f |
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1302 ] | |
1303 } | |
1304 }, | |
1305 "headers": [ | |
1306 ["rate", "Mean posterior relative rate at a site"], | |
1307 ["bias", "Mean posterior bias parameter at a site"], | |
1308 ["Prob[bias>0]", "Posterior probability of substitution bias"], | |
1309 ["BayesFactor[bias>0]", "Empiricial Bayes Factor for substitution bias"] | |
1310 ] | |
1311 }, | |
1312 "analysis":{ | |
1313 "authors":"Sergei L Kosakovsky Pond", | |
1314 "citation":"TBD", | |
1315 "contact":"spond@temple.edu", | |
1316 "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.", | |
1317 "requirements":"A protein alignment and a **rooted** phylogenetic tree (optionally annotated with {})", | |
1318 "version":"0.2" | |
1319 }, | |
1320 "branch attributes":{ | |
1321 "0":{ | |
1322 "EPI_ISL_1181694_HCOV_19_USA_DE_DHSS_B1064373_2021":{ | |
1323 "GTR":0, | |
1324 "original name":"EPI_ISL_1181694/HCOV-19/USA/DE-DHSS-B1064373/2021" | |
1325 }, | |
1326 "EPI_ISL_1284652_HCOV_19_GERMANY_SN_RKI_I_038291_2021":{ | |
1327 "GTR":0, | |
1328 "original name":"EPI_ISL_1284652/HCOV-19/GERMANY/SN-RKI-I-038291/2021" | |
1329 }, | |
1330 "EPI_ISL_1442952_HCOV_19_SINGAPORE_321_2021":{ | |
1331 "GTR":0.009544406421889584, | |
1332 "original name":"EPI_ISL_1442952/HCOV-19/SINGAPORE/321/2021" | |
1333 }, | |
1334 "EPI_ISL_1470937_HCOV_19_USA_NY_PRL_2021_03_29_01C17_2021":{ | |
1335 "GTR":0, | |
1336 "original name":"EPI_ISL_1470937/HCOV-19/USA/NY-PRL-2021_03_29_01C17/2021" | |
1337 }, | |
1338 "EPI_ISL_1512225_HCOV_19_USA_GA_CDC_STM_000041012_2021":{ | |
1339 "GTR":0.02186972306637773, | |
1340 "original name":"EPI_ISL_1512225/HCOV-19/USA/GA-CDC-STM-000041012/2021" | |
1341 }, | |
1342 "EPI_ISL_1516887_HCOV_19_AUSTRALIA_QLD1826_2021":{ | |
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1880 "original name":"GB_MW560924_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_CA_LACPHL_AF00280_2021_SEGMENT_NULL_HOST_HUMAN" | |
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1882 "GB_MW564865_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_CA_CZB_14906_2020_SEGMENT_NULL_HOST_HUMAN":{ | |
1883 "GTR":0, | |
1884 "original name":"GB_MW564865_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_CA_CZB_14906_2020_SEGMENT_NULL_HOST_HUMAN" | |
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1886 "GB_MW564882_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_CA_CZB_14886_2020_SEGMENT_NULL_HOST_HUMAN":{ | |
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1888 "original name":"GB_MW564882_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_CA_CZB_14886_2020_SEGMENT_NULL_HOST_HUMAN" | |
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1890 "GB_MW565403_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_CA_CZB_14413_2020_SEGMENT_NULL_HOST_HUMAN":{ | |
1891 "GTR":0, | |
1892 "original name":"GB_MW565403_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_CA_CZB_14413_2020_SEGMENT_NULL_HOST_HUMAN" | |
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1894 "GB_MW565438_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_CA_CZB_14344_2020_SEGMENT_NULL_HOST_HUMAN":{ | |
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1896 "original name":"GB_MW565438_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_CA_CZB_14344_2020_SEGMENT_NULL_HOST_HUMAN" | |
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1898 "GB_MW565832_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_MD_MDH_0724_2021_SEGMENT_NULL_HOST_HUMAN":{ | |
1899 "GTR":0, | |
1900 "original name":"GB_MW565832_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_MD_MDH_0724_2021_SEGMENT_NULL_HOST_HUMAN" | |
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1902 "GB_MW566477_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_CA_QDX_4490_2020_SEGMENT_NULL_HOST_HUMAN":{ | |
1903 "GTR":0, | |
1904 "original name":"GB_MW566477_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_CA_QDX_4490_2020_SEGMENT_NULL_HOST_HUMAN" | |
1905 }, | |
1906 "GB_MW566557_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_TX_QDX_4471_2020_SEGMENT_NULL_HOST_HUMAN":{ | |
1907 "GTR":0.02130032794036569, | |
1908 "original name":"GB_MW566557_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_TX_QDX_4471_2020_SEGMENT_NULL_HOST_HUMAN" | |
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1910 "GB_MW566849_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_FL_BPHL_2886_2020_SEGMENT_NULL_HOST_HUMAN":{ | |
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1912 "original name":"GB_MW566849_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_FL_BPHL_2886_2020_SEGMENT_NULL_HOST_HUMAN" | |
1913 }, | |
1914 "GB_MW566943_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_FL_BPHL_2980_2020_SEGMENT_NULL_HOST_HUMAN":{ | |
1915 "GTR":0, | |
1916 "original name":"GB_MW566943_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_FL_BPHL_2980_2020_SEGMENT_NULL_HOST_HUMAN" | |
1917 }, | |
1918 "GB_MW571108_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_GHA_WACCBIP_NCOV_GS49_2021_SEGMENT_NULL_HOST_HUMAN":{ | |
1919 "GTR":0.01258872651047252, | |
1920 "original name":"GB_MW571108_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_GHA_WACCBIP_NCOV_GS49_2021_SEGMENT_NULL_HOST_HUMAN" | |
1921 }, | |
1922 "GB_MW571118_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_GHA_WACCBIP_NCOV_GS145_2021_SEGMENT_NULL_HOST_HUMAN":{ | |
1923 "GTR":0.02130032756049533, | |
1924 "original name":"GB_MW571118_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_GHA_WACCBIP_NCOV_GS145_2021_SEGMENT_NULL_HOST_HUMAN" | |
1925 }, | |
1926 "GB_MW571185_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_GHA_WACCBIP_NCOV_GS69_2021_SEGMENT_NULL_HOST_HUMAN":{ | |
1927 "GTR":0, | |
1928 "original name":"GB_MW571185_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_GHA_WACCBIP_NCOV_GS69_2021_SEGMENT_NULL_HOST_HUMAN" | |
1929 }, | |
1930 "GB_MW578233_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_MD_MDH_0795_2021_SEGMENT_NULL_HOST_HUMAN":{ | |
1931 "GTR":0.02147417172573034, | |
1932 "original name":"GB_MW578233_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_MD_MDH_0795_2021_SEGMENT_NULL_HOST_HUMAN" | |
1933 }, | |
1934 "GB_MW578246_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_MD_MDH_0808_2021_SEGMENT_NULL_HOST_HUMAN":{ | |
1935 "GTR":0, | |
1936 "original name":"GB_MW578246_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_MD_MDH_0808_2021_SEGMENT_NULL_HOST_HUMAN" | |
1937 }, | |
1938 "GB_MW583187_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_OK_CDC_STM_000003021_2021_SEGMENT_NULL_HOST_HUMAN":{ | |
1939 "GTR":0, | |
1940 "original name":"GB_MW583187_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_OK_CDC_STM_000003021_2021_SEGMENT_NULL_HOST_HUMAN" | |
1941 }, | |
1942 "GB_MW583265_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_CA_CDC_STM_000001669_2021_SEGMENT_NULL_HOST_HUMAN":{ | |
1943 "GTR":0.02122042868986439, | |
1944 "original name":"GB_MW583265_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_CA_CDC_STM_000001669_2021_SEGMENT_NULL_HOST_HUMAN" | |
1945 }, | |
1946 "GB_MW585898_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_MA_CDC_STM_000003612_2021_SEGMENT_NULL_HOST_HUMAN":{ | |
1947 "GTR":0.02177267534968197, | |
1948 "original name":"GB_MW585898_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_MA_CDC_STM_000003612_2021_SEGMENT_NULL_HOST_HUMAN" | |
1949 }, | |
1950 "GB_MW586184_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_FL_CDC_STM_000005891_2021_SEGMENT_NULL_HOST_HUMAN":{ | |
1951 "GTR":0, | |
1952 "original name":"GB_MW586184_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_FL_CDC_STM_000005891_2021_SEGMENT_NULL_HOST_HUMAN" | |
1953 }, | |
1954 "GB_MW586256_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_FL_CDC_STM_000005477_2021_SEGMENT_NULL_HOST_HUMAN":{ | |
1955 "GTR":0.0213052439691005, | |
1956 "original name":"GB_MW586256_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_FL_CDC_STM_000005477_2021_SEGMENT_NULL_HOST_HUMAN" | |
1957 }, | |
1958 "GB_MW586274_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_TX_CDC_STM_000005611_2021_SEGMENT_NULL_HOST_HUMAN":{ | |
1959 "GTR":0, | |
1960 "original name":"GB_MW586274_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_TX_CDC_STM_000005611_2021_SEGMENT_NULL_HOST_HUMAN" | |
1961 }, | |
1962 "GB_MW586385_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_LA_CDC_STM_000005076_2021_SEGMENT_NULL_HOST_HUMAN":{ | |
1963 "GTR":0.02121636359237914, | |
1964 "original name":"GB_MW586385_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_LA_CDC_STM_000005076_2021_SEGMENT_NULL_HOST_HUMAN" | |
1965 }, | |
1966 "GB_MW586419_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_IA_CDC_STM_000005050_2021_SEGMENT_NULL_HOST_HUMAN":{ | |
1967 "GTR":0, | |
1968 "original name":"GB_MW586419_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_IA_CDC_STM_000005050_2021_SEGMENT_NULL_HOST_HUMAN" | |
1969 }, | |
1970 "GB_MW586670_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_FL_CDC_STM_000003618_2021_SEGMENT_NULL_HOST_HUMAN":{ | |
1971 "GTR":0.02121890219364495, | |
1972 "original name":"GB_MW586670_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_FL_CDC_STM_000003618_2021_SEGMENT_NULL_HOST_HUMAN" | |
1973 }, | |
1974 "GB_MW586700_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_CA_QDX_4173_2021_SEGMENT_NULL_HOST_HUMAN":{ | |
1975 "GTR":0.02101002190205874, | |
1976 "original name":"GB_MW586700_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_CA_QDX_4173_2021_SEGMENT_NULL_HOST_HUMAN" | |
1977 }, | |
1978 "GB_MW586846_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_NY_QDX_4256_2021_SEGMENT_NULL_HOST_HUMAN":{ | |
1979 "GTR":0.02122337052825341, | |
1980 "original name":"GB_MW586846_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_NY_QDX_4256_2021_SEGMENT_NULL_HOST_HUMAN" | |
1981 }, | |
1982 "GB_MW586849_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_PA_QDX_4292_2021_SEGMENT_NULL_HOST_HUMAN":{ | |
1983 "GTR":0.02763798357947539, | |
1984 "original name":"GB_MW586849_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_PA_QDX_4292_2021_SEGMENT_NULL_HOST_HUMAN" | |
1985 }, | |
1986 "GB_MW592637_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_MA_MASPHL_01774_2021_SEGMENT_NULL_HOST_HUMAN":{ | |
1987 "GTR":0.02130721832965677, | |
1988 "original name":"GB_MW592637_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_MA_MASPHL_01774_2021_SEGMENT_NULL_HOST_HUMAN" | |
1989 }, | |
1990 "GB_MW592782_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_MN_MDH_2311_2020_SEGMENT_NULL_HOST_HUMAN":{ | |
1991 "GTR":0.1786186183208891, | |
1992 "original name":"GB_MW592782_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_MN_MDH_2311_2020_SEGMENT_NULL_HOST_HUMAN" | |
1993 }, | |
1994 "GB_MW593179_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_FHCRC_1171_2020_SEGMENT_NULL_HOST_HUMAN":{ | |
1995 "GTR":0, | |
1996 "original name":"GB_MW593179_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_FHCRC_1171_2020_SEGMENT_NULL_HOST_HUMAN" | |
1997 }, | |
1998 "GB_MW593378_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_FHCRC_8518_2020_SEGMENT_NULL_HOST_HUMAN":{ | |
1999 "GTR":0.02155907100505753, | |
2000 "original name":"GB_MW593378_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_FHCRC_8518_2020_SEGMENT_NULL_HOST_HUMAN" | |
2001 }, | |
2002 "GB_MW593611_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_FHCRC_7938_2020_SEGMENT_NULL_HOST_HUMAN":{ | |
2003 "GTR":0, | |
2004 "original name":"GB_MW593611_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_FHCRC_7938_2020_SEGMENT_NULL_HOST_HUMAN" | |
2005 }, | |
2006 "GB_MW593708_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_FHCRC_4325_2020_SEGMENT_NULL_HOST_HUMAN":{ | |
2007 "GTR":0.02663904047039841, | |
2008 "original name":"GB_MW593708_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_FHCRC_4325_2020_SEGMENT_NULL_HOST_HUMAN" | |
2009 }, | |
2010 "GB_MW596234_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_LA_CDC_STM_000008248_2021_SEGMENT_NULL_HOST_HUMAN":{ | |
2011 "GTR":0, | |
2012 "original name":"GB_MW596234_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_LA_CDC_STM_000008248_2021_SEGMENT_NULL_HOST_HUMAN" | |
2013 }, | |
2014 "GB_MW598427_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_GHA_NMIMR_SARS_COV_2_NTRA_15010_2020_SEGMENT_NULL_HOST_HUMAN":{ | |
2015 "GTR":0.021547015910234, | |
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2017 }, | |
2018 "GB_MW599514_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_MA_BROAD_CRSP_00376_2021_SEGMENT_NULL_HOST_HUMAN":{ | |
2019 "GTR":0, | |
2020 "original name":"GB_MW599514_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_MA_BROAD_CRSP_00376_2021_SEGMENT_NULL_HOST_HUMAN" | |
2021 }, | |
2022 "GB_MW599662_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_RI_BROAD_RIDOH_00108_2020_SEGMENT_NULL_HOST_HUMAN":{ | |
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T_HUMAN,GB_MW206535_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_FL_BPHL_1865_2020_SEGMENT_NULL_HOST_HUMAN)Node342)Node336,((GB_MW583265_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_CA_CDC_STM_000001669_2021_SEGMENT_NULL_HOST_HUMAN,GB_MT969697_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_AUS_VIC2890_2020_SEGMENT_NULL_HOST_HUMAN)Node346,(GB_MW555931_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_WA_S3980_2021_SEGMENT_NULL_HOST_HUMAN,GB_MW566557_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_TX_QDX_4471_2020_SEGMENT_NULL_HOST_HUMAN)Node349)Node345)Node335)Node327)Node1,REFERENCE)" | |
2613 } | |
2614 }, | |
2615 "settings":{ | |
2616 "bayes factor":100, | |
2617 "burn-in":1000000, | |
2618 "chain-length":2000000, | |
2619 "chains":1, | |
2620 "concentration":0.5, | |
2621 "grid size":20, | |
2622 "method":"Variational-Bayes", | |
2623 "samples":100 | |
2624 }, | |
2625 "site annotations":{ | |
2626 "headers":{ | |
2627 "Composition":"Amino acid composition of site", | |
2628 "Substitutions":"Substitution history on selected branches" | |
2629 }, | |
2630 "site annotations":{ | |
2631 "0": [ | |
2632 ["M12", ""], | |
2633 ["F12", ""], | |
2634 ["H12", ""], | |
2635 ["L12", ""], | |
2636 ["V12", ""], | |
2637 ["D11,G1", "D->G(1)"], | |
2638 ["F12", ""], | |
2639 ["H1,Q11", "Q->H(1)"], | |
2640 ["V12", ""], | |
2641 ["T12", ""], | |
2642 ["I12", ""], | |
2643 ["A12", ""], | |
2644 ["E12", ""], | |
2645 ["I12", ""], | |
2646 ["L12", ""], | |
2647 ["L12", ""], | |
2648 ["I12", ""], | |
2649 ["I12", ""], | |
2650 ["M12", ""], | |
2651 ["K1,R10,S1", "R->K(1)S(1)"], | |
2652 ["T12", ""], | |
2653 ["F12", ""], | |
2654 ["K12", ""], | |
2655 ["F1,V11", "V->F(1)"], | |
2656 ["S12", ""], | |
2657 ["I12", ""], | |
2658 ["W12", ""], | |
2659 ["N12", ""], | |
2660 ["L12", ""], | |
2661 ["D12", ""], | |
2662 ["Y12", ""], | |
2663 ["I12", ""], | |
2664 ["I11,T1", ""], | |
2665 ["N12", ""], | |
2666 ["L12", ""], | |
2667 ["I12", ""], | |
2668 ["I12", ""], | |
2669 ["K12", ""], | |
2670 ["N12", ""], | |
2671 ["L12", ""], | |
2672 ["F1,S11", "C->F(1)"], | |
2673 ["K12", ""], | |
2674 ["S12", ""], | |
2675 ["L12", ""], | |
2676 ["T12", ""], | |
2677 ["E12", ""], | |
2678 ["N12", ""], | |
2679 ["K12", ""], | |
2680 ["Y12", ""], | |
2681 ["S12", ""], | |
2682 ["Q12", ""], | |
2683 ["L12", ""], | |
2684 ["D12", ""], | |
2685 ["E12", ""], | |
2686 ["E12", ""], | |
2687 ["Q12", ""], | |
2688 ["L1,P11", "P->L(1)"], | |
2689 ["M12", ""], | |
2690 ["E12", ""], | |
2691 ["I12", ""], | |
2692 ["C1,D11", "Y->C(1)"] | |
2693 ] | |
2694 } | |
2695 }, | |
2696 "tested":{ | |
2697 "0":{ | |
2698 "EPI_ISL_1181694_HCOV_19_USA_DE_DHSS_B1064373_2021":"test", | |
2699 "EPI_ISL_1284652_HCOV_19_GERMANY_SN_RKI_I_038291_2021":"test", | |
2700 "EPI_ISL_1442952_HCOV_19_SINGAPORE_321_2021":"test", | |
2701 "EPI_ISL_1470937_HCOV_19_USA_NY_PRL_2021_03_29_01C17_2021":"test", | |
2702 "EPI_ISL_1512225_HCOV_19_USA_GA_CDC_STM_000041012_2021":"test", | |
2703 "EPI_ISL_1516887_HCOV_19_AUSTRALIA_QLD1826_2021":"test", | |
2704 "EPI_ISL_1533793_HCOV_19_INDIA_MH_NCCS_CHN21027888_2021":"test", | |
2705 "EPI_ISL_1533799_HCOV_19_INDIA_MH_NCCS_9947_2021":"test", | |
2706 "EPI_ISL_1543980_HCOV_19_SINGAPORE_490_2021":"test", | |
2707 "EPI_ISL_1589923_HCOV_19_INDIA_WB_1930300571091_2021":"test", | |
2708 "EPI_ISL_1589926_HCOV_19_INDIA_WB_1930300586246_2021":"test", | |
2709 "EPI_ISL_1631286_HCOV_19_ENGLAND_CAMC_14E7527_2021":"test", | |
2710 "GB_LC571023_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_DP0724_SEGMENT_NULL_HOST_HUMAN":"background", | |
2711 "GB_MT326182_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_CT_UW_1365_2020_SEGMENT_NULL_HOST_HUMAN":"background", | |
2712 "GB_MT358638_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_DEU_FFM1_2020_SEGMENT_NULL_HOST_HUMAN":"background", | |
2713 "GB_MT359866_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_ESP_VH198152683_2020_SEGMENT_NULL_HOST_HUMAN":"background", | |
2714 "GB_MT447156_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_THA_SI200383_NT_2020_SEGMENT_NULL_HOST_HUMAN":"background", | |
2715 "GB_MT449654_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_CA_CZB_1063_2020_SEGMENT_NULL_HOST_HUMAN":"background", | |
2716 "GB_MT451104_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_AUS_VIC203_2020_SEGMENT_NULL_HOST_HUMAN":"background", | |
2717 "GB_MT520188_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_MA_MGH_00184_2020_SEGMENT_NULL_HOST_HUMAN":"background", | |
2718 "GB_MT520493_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_MA_MGH_00316_2020_SEGMENT_NULL_HOST_HUMAN":"background", | |
2719 "GB_MT601276_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_BGD_BCSIR_NILMRC_52_2020_SEGMENT_NULL_HOST_HUMAN":"background", | |
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3052 "timers":{ | |
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3081 "Residue G analysis":{ | |
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3090 "order":21, | |
3091 "timer":5 | |
3092 }, | |
3093 "Residue K analysis":{ | |
3094 "order":21, | |
3095 "timer":5 | |
3096 }, | |
3097 "Residue L analysis":{ | |
3098 "order":21, | |
3099 "timer":6 | |
3100 }, | |
3101 "Residue M analysis":{ | |
3102 "order":21, | |
3103 "timer":5 | |
3104 }, | |
3105 "Residue N analysis":{ | |
3106 "order":21, | |
3107 "timer":5 | |
3108 }, | |
3109 "Residue P analysis":{ | |
3110 "order":21, | |
3111 "timer":5 | |
3112 }, | |
3113 "Residue Q analysis":{ | |
3114 "order":21, | |
3115 "timer":5 | |
3116 }, | |
3117 "Residue R analysis":{ | |
3118 "order":21, | |
3119 "timer":6 | |
3120 }, | |
3121 "Residue S analysis":{ | |
3122 "order":21, | |
3123 "timer":5 | |
3124 }, | |
3125 "Residue T analysis":{ | |
3126 "order":21, | |
3127 "timer":5 | |
3128 }, | |
3129 "Residue V analysis":{ | |
3130 "order":21, | |
3131 "timer":5 | |
3132 }, | |
3133 "Residue W analysis":{ | |
3134 "order":21, | |
3135 "timer":5 | |
3136 }, | |
3137 "Residue Y analysis":{ | |
3138 "order":21, | |
3139 "timer":5 | |
3140 } | |
3141 } | |
3142 } |