Mercurial > repos > iuc > hyphy_summary
view test-data/busted-out2-1.json @ 4:11fc6218365d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 9ef881c2d3d5f240cbff33667b55f72cb82d9896"
author | iuc |
---|---|
date | Tue, 05 Oct 2021 05:09:34 +0000 |
parents | f304c108aa1f |
children | 11dd1a96ffe9 |
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episodic selection*, Mol Biol Evol. 32(5):1365-71", "contact":"spond@temple.edu", "info":"BUSTED (branch-site unrestricted statistical test of episodic diversification) uses a random effects branch-site model fitted \njointly to all or a subset of tree branches in order to test for alignment-wide evidence of episodic diversifying selection. \nAssuming there is evidence of positive selection (i.e. there is an omega > 1), BUSTED will also perform a quick evidence-ratio \nstyle analysis to explore which individual sites may have been subject to selection. v2.0 adds support for synonymous rate variation, \nand relaxes the test statistic to 0.5 (chi^2_0 + chi^2_2). Version 2.1 adds a grid search for the initial starting point.\nVersion 2.2 changes the grid search to LHC, and adds an initial search phase to use adaptive Nedler-Mead. Version 3.0 implements the option\nfor branch-site variation in synonymous substitution rates. Version 3.1 adds HMM auto-correlation option for SRV, and binds SRV distributions for multiple branch sets\n", "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})", "version":"3.1" }, "background":0, "branch attributes":{ "0":{ "B_FR_83_HXB2":{ "MG94xREV with separate rates for branch sets":0.01243274064118979, "Nucleotide GTR":0.01178680392701259, "constrained":0.01256398347964253, "original name":"B_FR_83_HXB2", "unconstrained":0.01346367617740634 }, "B_US_83_RF":{ "MG94xREV with separate rates for branch sets":0.02861520854418918, "Nucleotide GTR":0.02637179869727959, "constrained":0.02907713203932123, "original name":"B_US_83_RF", "unconstrained":0.03296423032791345 }, "B_US_86_JRFL":{ "MG94xREV with separate rates for branch sets":0.01913497611653954, "Nucleotide GTR":0.01766254318226218, "constrained":0.01932498128977916, "original name":"B_US_86_JRFL", "unconstrained":0.02067264364489925 }, "B_US_90_WEAU160":{ "MG94xREV with separate rates for branch sets":0.02258152057123029, "Nucleotide GTR":0.0208836028381146, "constrained":0.02318748492797678, "original name":"B_US_90_WEAU160", "unconstrained":0.02519768979779986 }, "D_CD_83_ELI":{ "MG94xREV with separate rates for branch sets":0.02096470337130958, "Nucleotide GTR":0.01905599613120992, "constrained":0.02057807476219352, "original name":"D_CD_83_ELI", "unconstrained":0.02169258688744172 }, "D_CD_83_NDK":{ "MG94xREV with separate rates for branch sets":0.01034012674036274, "Nucleotide GTR":0.009776698714183414, "constrained":0.0105101167818647, "original name":"D_CD_83_NDK", "unconstrained":0.01040169158313715 }, "D_CD_84_84ZR085":{ "MG94xREV with separate rates for branch sets":0.03124894063248942, "Nucleotide GTR":0.02822254903672137, "constrained":0.03140845141419388, "original name":"D_CD_84_84ZR085", "unconstrained":0.03388014669054998 }, "D_UG_94_94UG114":{ "MG94xREV with separate rates for branch sets":0.0597102708893009, "Nucleotide GTR":0.05323070232023583, "constrained":0.06218362660429492, "original name":"D_UG_94_94UG114", "unconstrained":0.06804948826756697 }, "Node1":{ "MG94xREV with separate rates for branch sets":0.02639559777106507, "Nucleotide GTR":0.02355240508560319, "constrained":0.02779997592087442, "unconstrained":0.02940126303315396 }, "Node10":{ "MG94xREV with separate rates for branch sets":0.00193736936681532, "Nucleotide GTR":0.002230248981703367, "constrained":0.001848018461605612, "unconstrained":0.001859856019153286 }, "Node2":{ "MG94xREV with separate rates for branch sets":0.003944601108756816, "Nucleotide GTR":0.003949360371801276, "constrained":0.00346172246250584, "unconstrained":0.002261770932022259 }, "Node3":{ "MG94xREV with separate rates for branch sets":0.01136485742287924, "Nucleotide GTR":0.01048442975058683, "constrained":0.01170820974676507, "unconstrained":0.01401270546560647 }, "Node9":{ "MG94xREV with separate rates for branch sets":0.005522231785763113, "Nucleotide GTR":0.004986123424162501, "constrained":0.005522033787153708, "unconstrained":0.005520113121560347 } }, "attributes":{ "MG94xREV with separate rates for branch sets":{ "attribute type":"branch length", "display order":1 }, "Nucleotide GTR":{ "attribute type":"branch length", "display order":0 }, "constrained":{ "attribute type":"branch length", "display order":1 }, "original name":{ "attribute type":"node label", "display order":0 }, "unconstrained":{ "attribute type":"branch length", "display order":0 } } }, "data partitions":{ "0":{ "coverage": [ [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, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439] ], "name":"busted.filter.default" } }, "fits":{ "Constrained model":{ "AIC-c":6398.612664722735, "Log Likelihood":-3168.021928691643, "Rate Distributions":{ "Test":{ "0":{ "omega":0, "proportion":0.6914129319908371 }, "1":{ "omega":0, "proportion":0.07568144722655729 }, "2":{ "omega":1, "proportion":0.2329056207826056 } } }, "display order":3, "estimated parameters":31 }, "MG94xREV with separate rates for branch sets":{ "AIC-c":6408.899382280021, "Equilibrium frequencies": [ [0.07535940345366139], [0.01443006409728228], [0.02915821068672351], [0.02954870567752823], [0.03219408024958758], [0.006164627375802654], [0.01245659774045292], [0.01262342001471309], [0.0276793164843978], [0.005300125700761717], [0.01070973633984303], [0.01085316415297191], [0.0418125103783387], [0.008006395714089126], [0.01617817990958604], [0.0163948426631036], [0.0409913146415633], [0.007849150478922548], [0.01586044121725868], [0.01607284872448998], [0.01751178502783737], [0.003353213651232053], [0.006775694789785172], [0.006866436807635995], [0.01505600521072376], [0.002882972930821469], [0.005825499564956559], [0.005903516300053625], [0.02274367484777162], [0.004355032959661065], [0.008800028033786655], [0.008917880494044083], [0.06143704799998004], [0.01176416611541591], [0.0237713451467977], [0.0240896977132239], [0.0262463496652457], [0.005025736545566795], [0.01015528996016046], [0.01029129247081581], [0.02256567087217255], [0.004320948178469224], [0.008731154380523415], [0.00884808446536876], [0.034087812394816], [0.006527245376826684], [0.01318932435908579], [0.01336595951511979], [0.01178447449308153], [0.02413128354890585], [0.0262916585104385], [0.005034412430862358], [0.01017282094890981], [0.01030905823951665], [0.004328407393735399], [0.008746226896405704], [0.008863358836639712], [0.03414665788893068], [0.006538513303760755], [0.0132120929750345], [0.01338903305480236] ], "Log Likelihood":-3176.217093030587, "Rate Distributions":{ "non-synonymous/synonymous rate ratio for *test*": [ [0.231720664913378, 1] ] }, "display order":1, "estimated parameters":28 }, "Nucleotide GTR":{ "AIC-c":6683.094244259512, "Equilibrium frequencies": [ [0.4044507575757576], [0.1662878787878788], [0.2095643939393939], [0.2196969696969697] ], "Log Likelihood":-3320.503280793639, "Rate Distributions":{ "Substitution rate from nucleotide A to nucleotide C":0.1815218119292989, "Substitution rate from nucleotide A to nucleotide G":1, "Substitution rate from nucleotide A to nucleotide T":0.08433479296165451, "Substitution rate from nucleotide C to nucleotide G":0.1775869374255926, "Substitution rate from nucleotide C to nucleotide T":1.184827038118431, "Substitution rate from nucleotide G to nucleotide T":0.04288318031815568 }, "display order":0, "estimated parameters":21 }, "Unconstrained model":{ "AIC-c":6391.938375474656, "Log Likelihood":-3163.666348620609, "Rate Distributions":{ "Test":{ "0":{ "omega":0.1490485393860332, "proportion":0.02658974082564446 }, "1":{ "omega":0.169565784922581, "proportion":0.9641001770967245 }, "2":{ "omega":15.09387961636913, "proportion":0.009310082077631076 } } }, "display order":2, "estimated parameters":32 } }, "input":{ "file name":"/tmp/tmpfqvtss8b/job_working_directory/000/5/working/./input.nex", "number of sequences":8, "number of sites":440, "partition count":1, "trees":{ "0":"((((D_CD_83_ELI,D_CD_83_NDK)Node3,D_UG_94_94UG114)Node2,D_CD_84_84ZR085)Node1,B_US_83_RF,((B_FR_83_HXB2,B_US_86_JRFL)Node10,B_US_90_WEAU160)Node9)" } }, "test results":{ "LRT":8.711160142067456, "p-value":0.006417496108925114 }, "tested":{ "0":{ "B_FR_83_HXB2":"test", "B_US_83_RF":"test", "B_US_86_JRFL":"test", "B_US_90_WEAU160":"test", "D_CD_83_ELI":"test", "D_CD_83_NDK":"test", "D_CD_84_84ZR085":"test", "D_UG_94_94UG114":"test", "Node1":"test", "Node10":"test", "Node2":"test", "Node3":"test", "Node9":"test" } }, "timers":{ "Constrained BUSTED model fitting":{ "order":3, "timer":23 }, "Overall":{ "order":0, "timer":133 }, "Preliminary model fitting":{ "order":1, "timer":4 }, "Unconstrained BUSTED model fitting":{ "order":2, "timer":105 } } }