Mercurial > repos > iuc > hyphy_conv
diff test-data/busted-out1.json @ 2:f6e7b5955712 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
| author | iuc |
|---|---|
| date | Tue, 27 Apr 2021 18:02:47 +0000 |
| parents | 9ce3d6d4bd0e |
| children |
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--- a/test-data/busted-out1.json Tue Apr 20 19:55:16 2021 +0000 +++ b/test-data/busted-out1.json Tue Apr 27 18:02:47 2021 +0000 @@ -1,73 +1,73 @@ { "Evidence Ratios":{ "constrained": [ -[1.766356514902524, 0.9484374805763239, 0.9571091930814299, 1.845676838710576, 1.513819401189324, 2.11256226458989, 7.366103227625151, 3.937756516229049, 2.586067836907899, 0.722379841928909, 0.3151239046214458, 1.502917468627881, 0.6499879033472316, 1.047489715978757, 1.060206108705189, 0.5038296392390414, 0.8532658611088545, 1.114374823999701, 0.5611409841208096, 0.6702870396165613, 0.4604115167079821, 0.3988433224622866, 2.47019807349414, 0.9858342091732886, 1.106653406611749, 1.067348070135177, 1.77412165088655, 1.321424873505688, 1.90457149631063, 0.7888758683589224, 0.7229203540914775, 0.8813401886687667, 0.6954297746421804, 4.613654710605887, 0.4975309466317643, 1.84565076502724, 0.6214894235132998, 0.9480915704528677, 0.9669462933548731, 1.488081789562878, 1.368539685217942, 1.726522735566884, 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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\n", + "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":"3.0" + "version":"3.1" }, "background":0, "branch attributes":{ "0":{ "Baboon":{ - "MG94xREV with separate rates for branch sets":0.001771850913718116, - "Nucleotide GTR":0.00167976779100812, - "constrained":0.0005055252388761481, + "MG94xREV with separate rates for branch sets":0.001772434847524003, + "Nucleotide GTR":0.001680040630127455, + "constrained":0.001513413708231178, "original name":"Baboon", - "unconstrained":0.0005398732671668005 + "unconstrained":0.00161713005248515 }, "Cat":{ - "MG94xREV with separate rates for branch sets":0.2738959056554072, - "Nucleotide GTR":0.266075486389923, - "constrained":0.1152712488116292, + "MG94xREV with separate rates for branch sets":0.2735065373507703, + "Nucleotide GTR":0.2660909938917123, + "constrained":0.3466844629529476, "original name":"Cat", - 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"unconstrained":0.08275992348314189 + "unconstrained":0.248176820169511 }, "Rat":{ - "MG94xREV with separate rates for branch sets":0.06698958986289986, - "Nucleotide GTR":0.06656862018951525, - "constrained":0.02277034233250765, + "MG94xREV with separate rates for branch sets":0.06699144002108472, + "Nucleotide GTR":0.06661283005976348, + "constrained":0.06832918896283274, "original name":"Rat", - "unconstrained":0.02372534359054489 + "unconstrained":0.07114161288708017 }, "RhMonkey":{ - "MG94xREV with separate rates for branch sets":0.003717482368324115, - "Nucleotide GTR":0.003775504255522691, - "constrained":0.001359450941376631, + "MG94xREV with separate rates for branch sets":0.003716234330029482, + "Nucleotide GTR":0.003775170135617877, + "constrained":0.004078975866589158, "original name":"RhMonkey", - "unconstrained":0.00132482447204072 + "unconstrained":0.003977618821878279 } }, "attributes":{ @@ -174,35 +174,35 @@ }, "fits":{ "Constrained model":{ - "AIC-c":6918.851822592964, - "Log Likelihood":-3419.573452280089, + "AIC-c":6918.865252134614, + "Log Likelihood":-3419.580167050914, "Rate Distributions":{ "Synonymous site-to-site rates":{ "0":{ - "proportion":0.3289898788632067, - "rate":0.3124849036133048 + "proportion":0.3286044813984554, + "rate":0.3114745230555425 }, "1":{ - "proportion":0.5748197734913485, - "rate":1.039520868895482 + "proportion":0.5759073485616787, + "rate":1.038727366194607 }, "2":{ - "proportion":0.09619034764544485, - "rate":3.115265578623139 + "proportion":0.09548817003986594, + "rate":3.135858111155513 } }, "Test":{ "0":{ "omega":0, - "proportion":0.02093092071081848 + "proportion":0.1610337459523823 }, "1":{ - "omega":0, - "proportion":0.1387433808480476 + "omega":0.9239856235614761, + "proportion":0 }, "2":{ "omega":1, - "proportion":0.8403256984411339 + "proportion":0.8389662540476177 } } }, @@ -210,129 +210,129 @@ "estimated parameters":39 }, "MG94xREV with separate rates for branch sets":{ - "AIC-c":6997.089050462658, + "AIC-c":6997.104847699299, "Equilibrium frequencies": [ -[0.04875339327772683], - 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"Log Likelihood":-3467.004808147542, + "Log Likelihood":-3467.012706765863, "Rate Distributions":{ "non-synonymous/synonymous rate ratio for *test*": [ -[0.9950576192409499, 1] +[0.9959842858928788, 1] ] }, "display order":1, "estimated parameters":31 }, "Nucleotide GTR":{ - "AIC-c":7112.85745601076, + "AIC-c":7112.857310169033, "Equilibrium frequencies": [ [0.3592490842490842], [0.181959706959707], [0.240018315018315], [0.2187728937728937] ], - "Log Likelihood":-3532.321297387654, + "Log Likelihood":-3532.32122446679, "Rate Distributions":{ - "Substitution rate from nucleotide A to nucleotide C":0.5497129763145497, + "Substitution rate from nucleotide A to nucleotide C":0.5501644800943087, "Substitution rate from nucleotide A to nucleotide G":1, - "Substitution rate from nucleotide A to nucleotide T":0.264666902964203, - "Substitution rate from nucleotide C to nucleotide G":0.4916303643305098, - "Substitution rate from nucleotide C to nucleotide T":1.027924764411573, - "Substitution rate from nucleotide G to nucleotide T":0.304615404570875 + "Substitution rate from nucleotide A to nucleotide T":0.2647746107611847, + "Substitution rate from nucleotide C to nucleotide G":0.4917423221832032, + "Substitution rate from nucleotide C to nucleotide T":1.02837595903795, + "Substitution rate from nucleotide G to nucleotide T":0.304509117524575 }, "display order":0, "estimated parameters":24 }, "Unconstrained model":{ - "AIC-c":6910.766610587704, - "Log Likelihood":-3414.486640449675, + "AIC-c":6910.776988890891, + "Log Likelihood":-3414.491829601268, "Rate Distributions":{ "Synonymous site-to-site rates":{ "0":{ - "proportion":0.2645541257391169, - "rate":0.2747941124675511 + "proportion":0.2655037162058198, + "rate":0.2749303122566129 }, "1":{ - "proportion":0.6325830460054784, - "rate":0.9734675888351726 + "proportion":0.6321791898264187, + "rate":0.9740711294478059 }, "2":{ - "proportion":0.1028628282554047, - "rate":3.028333913894314 + "proportion":0.1023170939677615, + "rate":3.041695877803997 } }, "Test":{ "0":{ "omega":0, - "proportion":0.04809457608200497 + "proportion":0.386646389823596 }, "1":{ - "omega":0, - "proportion":0.3410012743721951 + "omega":0.9964438830494696, + "proportion":0 }, "2":{ - "omega":1.89363684081788, - "proportion":0.6109041495458 + "omega":1.876622752045829, + "proportion":0.613353610176404 } } }, @@ -341,7 +341,7 @@ } }, "input":{ - "file name":"/tmp/tmp7qHfo2/job_working_directory/000/3/working/./busted_input.fa", + "file name":"/tmp/tmpfqvtss8b/job_working_directory/000/3/working/./input.fasta", "number of sequences":10, "number of sites":187, "partition count":1, @@ -350,8 +350,8 @@ } }, "test results":{ - "LRT":10.17362366082671, - "p-value":0.003088842014430382 + "LRT":10.17667489929045, + "p-value":0.003084133210483175 }, "tested":{ "0":{ @@ -376,19 +376,19 @@ "timers":{ "Constrained BUSTED model fitting":{ "order":3, - "timer":62 + "timer":70 }, "Overall":{ "order":0, - "timer":228 + "timer":451 }, "Preliminary model fitting":{ "order":1, - "timer":3 + "timer":10 }, "Unconstrained BUSTED model fitting":{ "order":2, - "timer":161 + "timer":370 } } } \ No newline at end of file