Mercurial > repos > iuc > hyphy_cfel
view test-data/relax-out2-1.json @ 3:c046f72e5e3a draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
author | iuc |
---|---|
date | Wed, 09 Jun 2021 06:58:21 +0000 |
parents | fb833dd994f2 |
children | 5b63871000c9 |
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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] ], "name":"relax.filter.default" } }, "fits":{ "General descriptive":{ "AIC-c":6945.891070751259, "Log Likelihood":-3420.486789501042, "Rate Distributions":{ "Shared":{ "0":{ "omega":2.20271427504516e-18, "proportion":0.00789425874100967 }, "1":{ "omega":2.20271427504516e-18, "proportion":0.5381203586928067 }, "2":{ "omega":2.202714092571507, "proportion":0.4539853825661836 } } }, "display order":4, "estimated parameters":51 }, "MG94xREV with separate rates for branch sets":{ "AIC-c":6987.278662183248, "Equilibrium frequencies": [ [0.04876086397632926], [0.03982224127745371], [0.0494959405650269], [0.04152830682371345], [0.01810345074594235], [0.01478480742075003], [0.01837636270304883], [0.01541821854326533], [0.01892910005547028], [0.01545910240515689], [0.01921445878706794], [0.01612140169177368], [0.02829747763884322], [0.02311011106415996], [0.02872406592369408], [0.02410019507229243], [0.01663805943190806], [0.01358804506433061], [0.01688888041768248], [0.01417018446135155], [0.006177213955434187], [0.005044834822351987], [0.006270336287397383], [0.00526096577332031], [0.006458939937330408], [0.005274916061901906], [0.006556309326397028], [0.005500904159606446], 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"display order":1, "estimated parameters":32 }, "Nucleotide GTR":{ "AIC-c":7112.857310169033, "Equilibrium frequencies": [ [0.3592490842490842], [0.181959706959707], [0.240018315018315], [0.2187728937728937] ], "Log Likelihood":-3532.32122446679, "Rate Distributions":{ "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":0.2647746107611847, "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 }, "RELAX alternative":{ "AIC-c":6901.392449196474, "Log Likelihood":-3408.754211469135, "Rate Distributions":{ "Reference":{ "0":{ "omega":0, "proportion":0.3814061972635792 }, "1":{ "omega":0.4330262245823013, "proportion":0 }, "2":{ "omega":2.405594515133199, "proportion":0.6185938027364208 } }, "Synonymous site-to-site rates":{ "0":{ "proportion":0.2800901562602482, "rate":0.2837970682663188 }, "1":{ "proportion":0.6272754947629234, "rate":0.9947075941569237 }, "2":{ "proportion":0.09263434897682828, "rate":3.20135608237551 } }, "Test":{ "0":{ "omega":0, "proportion":0.3814061972635792 }, "1":{ "omega":0.9999750044281671, "proportion":0 }, "2":{ "omega":1.00002621592498, "proportion":0.6185938027364208 } } }, "display order":2, "estimated parameters":41 }, "RELAX null":{ "AIC-c":6910.777215627525, "Log Likelihood":-3414.491942969586, "Rate Distributions":{ "Reference":{ "0":{ "omega":0, "proportion":0.04600287725570656 }, "1":{ "omega":0, "proportion":0.3432466763494891 }, "2":{ "omega":1.896477292815783, "proportion":0.6107504463948045 } }, "Synonymous site-to-site rates":{ "0":{ "proportion":0.2641095265325168, "rate":0.2744837794048847 }, "1":{ "proportion":0.6330324513232739, "rate":0.9729462345446451 }, "2":{ "proportion":0.1028580221442092, "rate":3.029415427453047 } }, "Test":{ "0":{ "omega":0, "proportion":0.04600287725570656 }, "1":{ "omega":0, "proportion":0.3432466763494891 }, "2":{ "omega":1.896477292815783, "proportion":0.6107504463948045 } } }, "display order":3, "estimated parameters":40 }, "RELAX partitioned descriptive":{ "AIC-c":6909.42794543134, "Log Likelihood":-3408.579104294618, "Rate Distributions":{ "Reference":{ "0":{ "omega":0.05035684771569529, "proportion":0.3805224005150026 }, "1":{ "omega":0.07013486723985318, "proportion":0.003462124163764896 }, "2":{ "omega":2.344944921144001, "proportion":0.6160154753212325 } }, "Test":{ "0":{ "omega":0, "proportion":0.03160127773820932 }, "1":{ "omega":0, "proportion":0.4079248249859382 }, "2":{ "omega":1.11269394570475, "proportion":0.5604738972758525 } } }, "display order":5, "estimated parameters":45 } }, "input":{ "file name":"/tmp/tmpbauyxvdv/job_working_directory/000/5/working/./input.nex", "number of sequences":10, "number of sites":187, "partition count":1, "trees":{ "0":"((((PIG:0.147969,COW:0.21343)Node3:0.08509899999999999,HORSE:0.165787,CAT:0.264806)Node2:0.058611,((RHMONKEY:0.002015,BABOON:0.003108)Node9:0.022733,(HUMAN:0.004349,CHIMP:0.000799)Node12:0.011873)Node8:0.101856)Node1:0.340802,RAT:0.050958,MOUSE:0.09795)" } }, "test results":{ "LRT":11.47546300090198, "p-value":0.0007052107640865835, "relaxation or intensification parameter":2.986519568748539e-05 }, "tested":{ "0":{ "BABOON":"Test", "CAT":"Reference", "CHIMP":"Test", "COW":"Reference", "HORSE":"Reference", "HUMAN":"Test", "MOUSE":"Reference", "Node1":"Test", "Node12":"Test", "Node2":"Reference", "Node3":"Reference", "Node8":"Test", "Node9":"Test", "PIG":"Reference", "RAT":"Reference", "RHMONKEY":"Test" } }, "timers":{ "General descriptive model fitting":{ "order":2, "timer":127 }, "Overall":{ "order":0, "timer":645 }, "Preliminary model fitting":{ "order":1, "timer":8 }, "RELAX alternative model fitting":{ "order":3, "timer":178 }, "RELAX null model fitting":{ "order":4, "timer":115 }, "RELAX partitioned descriptive":{ "order":5, "timer":216 } } }