Mercurial > repos > iuc > hyphy_meme
view test-data/prime-out1.json @ 27:d653a76f16ee draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2063bc1f8f9cb97de147b86dbe9189fc496b206a"
author | iuc |
---|---|
date | Wed, 09 Jun 2021 17:31:49 +0000 |
parents | 3d1f153e2aa1 |
children |
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["FEL LogL", "Site Log-likelihood under the FEL model"], ["p-value", "Omnibus p-value (any property is important)"], ["λ1", "Importance for Factor I bipolar"], ["p1", "p-value for non-zero effect of Factor I bipolar"], ["LogL1", "Log likelihood when there is no effect of Factor I bipolar"], ["λ2", "Importance for Factor II secondary structure"], ["p2", "p-value for non-zero effect of Factor II secondary structure"], ["LogL2", "Log likelihood when there is no effect of Factor II secondary structure"], ["λ3", "Importance for Factor III volume"], ["p3", "p-value for non-zero effect of Factor III volume"], ["LogL3", "Log likelihood when there is no effect of Factor III volume"], ["λ4", "Importance for Factor IV composition"], ["p4", "p-value for non-zero effect of Factor IV composition"], ["LogL4", "Log likelihood when there is no effect of Factor IV composition"], ["λ5", "Importance for Factor V charge"], ["p5", "p-value for non-zero effect of Factor V charge"], ["LogL5", "Log likelihood when there is no effect of Factor V charge"] ] }, "analysis":{ "authors":"Sergei L. Kosakovsky Pond", "citation":"TBD", "contact":"spond@temple.edu", "info":"PRIME (PRoperty Informed Model of Evolution). Given a set of N amino-acid properties,\n fit a site-level model where non-synonymous rates depend on how much a non-synonymous substitution changes the \n properties of the residue, beta (X,Y) = Exp (log_omega - lambda_1 * diff_1 (X,Y )- lambda_2 * diff_2 (X,Y) -...).\n When lambda_k > 0, changes in property k are disfavored and when lambda_k < 0 -- they are promoted.\n At each site, N tests are performed\n A subset of branches can be selected\n for testing as well, in which case an additional (nuisance) parameter will be\n inferred -- the non-synonymous rate on branches NOT selected for testing. Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ", "requirements":"in-frame codon alignment and a phylogenetic tree", "version":"0.0.1" }, "branch attributes":{ "0":{ "CHICKEN_CK_160_2005":{ "Global MG94xREV":0.006875905528136641, "Nucleotide GTR":0.006740765844759078, "original name":"CHICKEN_CK_160_2005" }, "CHICKEN_HEBEI_326_2005":{ "Global MG94xREV":0.03000509055831138, "Nucleotide GTR":0.02817726192677478, "original name":"CHICKEN_HEBEI_326_2005" }, "CHICKEN_HONGKONG_915_97":{ "Global MG94xREV":0, "Nucleotide GTR":0, "original name":"CHICKEN_HONGKONG_915_97" }, "CK_HK_WF157_2003":{ "Global MG94xREV":0, "Nucleotide GTR":0, "original name":"CK_HK_WF157_2003" }, "GOOSE_HONGKONG_W355_97":{ "Global MG94xREV":0, "Nucleotide GTR":0, "original name":"GOOSE_HONGKONG_W355_97" }, "GOOSE_SHANTOU_2216_2005":{ "Global MG94xREV":0.008912012248907763, "Nucleotide GTR":0.007985902570718373, "original name":"GOOSE_SHANTOU_2216_2005" }, "HONGKONG_1_538_97":{ "Global MG94xREV":0, "Nucleotide GTR":0, "original name":"HONGKONG_1_538_97" }, "HONGKONG_1_97_98":{ "Global MG94xREV":0.02020234274992877, "Nucleotide GTR":0.02001220163799822, "original name":"HONGKONG_1_97_98" }, "HUMAN_VIETNAM_3062_2004":{ "Global MG94xREV":0, "Nucleotide GTR":0, "original name":"HUMAN_VIETNAM_3062_2004" }, "HUMAN_VIETNAM_CL105_2005":{ "Global MG94xREV":0.006025788919462983, "Nucleotide GTR":0.005802088014335368, "original name":"HUMAN_VIETNAM_CL105_2005" }, "MALLARD_VIETNAM_16_2003":{ "Global MG94xREV":0, "Nucleotide GTR":0, "original name":"MALLARD_VIETNAM_16_2003" }, "Node10":{ "Global MG94xREV":0, "Nucleotide GTR":0 }, "Node11":{ "Global MG94xREV":0, "Nucleotide GTR":0 }, "Node13":{ "Global MG94xREV":0, "Nucleotide GTR":0 }, "Node17":{ "Global MG94xREV":0, "Nucleotide GTR":0 }, "Node18":{ "Global MG94xREV":0, "Nucleotide GTR":0 }, "Node19":{ "Global MG94xREV":0.004922199772633382, "Nucleotide GTR":0.005534464552270369 }, "Node2":{ "Global MG94xREV":0.006872306486383904, "Nucleotide GTR":0.006718147482064949 }, "Node23":{ "Global MG94xREV":0, "Nucleotide GTR":0 }, "Node24":{ "Global MG94xREV":0, "Nucleotide GTR":0 }, "Node25":{ "Global MG94xREV":0.0008268367968756879, "Nucleotide GTR":0.0009189593587976459 }, "Node3":{ "Global MG94xREV":0, "Nucleotide GTR":0 }, "Node4":{ "Global MG94xREV":0.002648185777377607, "Nucleotide GTR":0.00251461257430795 }, "Node5":{ "Global MG94xREV":0.003268514528883674, "Nucleotide GTR":0.003965274251091903 }, "Node7":{ "Global MG94xREV":0.005023432525711092, "Nucleotide GTR":0.004793454999477672 }, "Node9":{ "Global MG94xREV":0.01391813691986412, "Nucleotide GTR":0.01351408611669037 }, "PEREGRINEFALCON_HK_D0028_2004":{ "Global MG94xREV":0.006920710269269024, "Nucleotide GTR":0.006722811033712868, "original name":"PEREGRINEFALCON_HK_D0028_2004" }, "SWINE_ANHUI_1_2004":{ "Global MG94xREV":0.01018798286684916, "Nucleotide GTR":0.009150633137551082, "original name":"SWINE_ANHUI_1_2004" } }, "attributes":{ "Global MG94xREV":{ "attribute type":"branch length", "display order":1 }, "Nucleotide GTR":{ "attribute type":"branch length", "display order":0 }, "original name":{ "attribute type":"node label", "display order":-1 } } }, "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] ], "name":"prime.filter.default" } }, "fits":{ "Global MG94xREV":{ "AIC-c":647.6795207053656, "Equilibrium frequencies": [ [0.04488063522282697], [0.02743154763030629], [0.03260676907658289], [0.05361444334761576], [0.01878621141548667], [0.0114823431236735], [0.01364859597925394], [0.02244202343953587], [0.00898846188937465], [0.005493848721556544], [0.006530315351495689], [0.01073762388516669], [0.04007728102844568], [0.02449568367218243], [0.02911702655775225], [0.04787635251947601], [0.02154103095825152], 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[0.006507708080284218], [0.01070045135026252] ], "Log Likelihood":-277.7176481414617, "Rate Distributions":{ "non-synonymous/synonymous rate ratio for *test*": [ [0.4074296362572946, 1] ] }, "display order":1, "estimated parameters":43 }, "Nucleotide GTR":{ "AIC-c":658.4548031196325, "Equilibrium frequencies": [ [0.3543689320388349], [0.1790722761596548], [0.2076591154261057], [0.2588996763754045] ], "Log Likelihood":-292.5311130078037, "Rate Distributions":{ "Substitution rate from nucleotide A to nucleotide C":0, "Substitution rate from nucleotide A to nucleotide G":1, "Substitution rate from nucleotide A to nucleotide T":0, "Substitution rate from nucleotide C to nucleotide G":0, "Substitution rate from nucleotide C to nucleotide T":1.816257034982832, "Substitution rate from nucleotide G to nucleotide T":0 }, "display order":0, "estimated parameters":36 } }, "input":{ "file name":"/Users/sergei/Development/tools-iuc/tools/hyphy/test-data/prime-in1.fa", "number of sequences":13, "number of sites":50, "partition count":1, "trees":{ "0":"(((((CHICKEN_HEBEI_326_2005:0.02100885319673648,(SWINE_ANHUI_1_2004:0.007702393698306516)Node7:0.002095219592954275)Node5:0.003887237703073042)Node4:0.003404921392531202,(((CHICKEN_HONGKONG_915_97:-1,(GOOSE_HONGKONG_W355_97:-1)Node13:0.002899766890966483)Node11:0.001306376767766534,HONGKONG_1_97_98:0.003844928589233716)Node10:0.000182535836694054,HONGKONG_1_538_97:-1)Node9:0.02096173714686362)Node3:0.003130608143291779,(((GOOSE_SHANTOU_2216_2005:0.006207842095177651)Node19:0.002530613798219486,PEREGRINEFALCON_HK_D0028_2004:0.003608296348267232)Node18:0.003288900909856382,CK_HK_WF157_2003:0.00663129750258774)Node17:0.004655295319725731)Node2:0.0116808817874948,(((HUMAN_VIETNAM_CL105_2005:0.006521522005742001)Node25:0.001967887030302483,HUMAN_VIETNAM_3062_2004:0.001641397323851184)Node24:0.0003125512332168847,MALLARD_VIETNAM_16_2003:0.003244216605281072)Node23:0.0004125980823087554,CHICKEN_CK_160_2005:0.006168335080088849)" } }, "tested":{ "0":{ "CHICKEN_CK_160_2005":"test", "CHICKEN_HEBEI_326_2005":"test", "CHICKEN_HONGKONG_915_97":"test", "CK_HK_WF157_2003":"test", "GOOSE_HONGKONG_W355_97":"test", "GOOSE_SHANTOU_2216_2005":"test", "HONGKONG_1_538_97":"test", "HONGKONG_1_97_98":"test", "HUMAN_VIETNAM_3062_2004":"test", "HUMAN_VIETNAM_CL105_2005":"test", "MALLARD_VIETNAM_16_2003":"test", "Node10":"test", "Node11":"test", "Node13":"test", "Node17":"test", "Node18":"test", "Node19":"test", "Node2":"test", "Node23":"test", "Node24":"test", "Node25":"test", "Node3":"test", "Node4":"test", "Node5":"test", "Node7":"test", "Node9":"test", "PEREGRINEFALCON_HK_D0028_2004":"test", "SWINE_ANHUI_1_2004":"test" } }, "timers":{ "Model fitting":{ "order":1, "timer":3 }, "PRIME analysis":{ "order":2, "timer":86 }, "Total time":{ "order":0, "timer":89 } } }