Mercurial > repos > iuc > hyphy_annotate

comparison test-data/summary/ORF6.FADE.json @ 12:6efabd37807b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
author iuc
date Tue, 07 Oct 2025 20:44:41 +0000
parents d088a1cca4a7
children
comparison
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11:d088a1cca4a7 12:6efabd37807b
1 {
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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 },
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2554 }
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2564 }
2565 }
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2568 "0":{
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2570 [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]
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2573 }
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2578 "Equilibrium frequencies": [
2579 [0.02812268730598148],
2580 [0.0009589862341044153],
2581 [0.05207996587706627],
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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",
2720 "GB_MT601281_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_BGD_BCSIR_NILMRC_67_2020_SEGMENT_NULL_HOST_HUMAN":"background",
2721 "GB_MT612186_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_AUS_VIC1576_2020_SEGMENT_NULL_HOST_HUMAN":"background",
2722 "GB_MT627613_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_WA_S260_2020_SEGMENT_NULL_HOST_HUMAN":"background",
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2800 "GB_MW490888_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_FL_BPHL_2295_2020_SEGMENT_NULL_HOST_HUMAN":"background",
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2802 "GB_MW491211_ORGANISM_SEVERE_ACUTE_RESPIRATORY_SYNDROME_CORONAVIRUS_2_STRAIN_NAME_SARS_COV_2_HUMAN_USA_FL_BPHL_2755_2020_SEGMENT_NULL_HOST_HUMAN":"background",
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