Mercurial > repos > iuc > hyphy_strike_ambigs
view test-data/fade-out1.json @ 10:f5bbd4b34541 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 821e0f3e4546bc55e093ab63bd9f9b57f2bf772d
| author | iuc |
|---|---|
| date | Thu, 18 Aug 2022 14:02:58 +0000 |
| parents | 7c86ceaf523c |
| children |
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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.", "requirements":"A protein alignment and a **rooted** phylogenetic tree (optionally annotated with {})", "version":"0.2" }, "branch attributes":{ "0":{ "Baboon":{ "GTR":0, "original name":"Baboon" }, "Cat":{ "GTR":0.5479738108231806, "original name":"Cat" }, "Chimp":{ "GTR":0.005354406956230157, "original name":"Chimp" }, "Cow":{ "GTR":0.5217716656054335, "original name":"Cow" }, "Horse":{ "GTR":0.3639593662085931, "original name":"Horse" }, "Human":{ "GTR":0, "original name":"Human" }, "Mouse":{ "GTR":0.1538063185305938, "original name":"Mouse" }, "Node1":{ "GTR":0.03774939091948738 }, "Node10":{ "GTR":0.04065491268006209 }, "Node13":{ "GTR":0.02528485699542644 }, "Node2":{ "GTR":0.4507260725563764 }, "Node3":{ "GTR":0.06938193079176812 }, "Node4":{ "GTR":0.2509978904573531 }, "Node9":{ "GTR":0.2259272621401927 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name":"/Users/ryanvelazquez/Documents/galaxy_items/tools-iuc/tools/hyphy/./test-data/fade-in1.fa", "number of sequences":10, "number of sites":187, "partition count":1, "trees":{ "0":"(((((Pig:0.147969,Cow:0.21343)Node4:0.08509899999999999,Horse:0.165787,Cat:0.264806)Node3:0.058611,((RhMonkey:0.002015,Baboon:0.003108)Node10:0.022733,(Human:0.004349,Chimp:0.000799)Node13:0.011873)Node9:0.101856)Node2:0.340802,Rat:0.050958)Node1:0.1,Mouse:0.09795)" } }, "settings":{ "bayes factor":100, "burn-in":1000000, "chain-length":2000000, "chains":1, "concentration":0.5, "grid size":20, "method":"Variational-Bayes", "samples":100 }, "site annotations":{ "headers":{ "Composition":"Amino acid composition of site", "Substitutions":"Substitution history on selected branches" }, "site annotations":{ "0": [ ["E1,K8", "K->E(1)"], ["E9", ""], ["I9", ""], ["A1,R6,T6", "R->T(1), T->A(1)R(1)"], ["D3,E1,K1,N11", "D->N(1), N->E(1)K(1)"], ["A7,D1,N5,S3,T1", "N->A(1)D(1)S(2), S->T(1)"], ["D1,E3,G1,I5,L7", 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} }, "tested":{ "0":{ "Baboon":"test", "Cat":"test", "Chimp":"test", "Cow":"test", "Horse":"test", "Human":"test", "Mouse":"test", "Node1":"test", "Node10":"test", "Node13":"test", "Node2":"test", "Node3":"test", "Node4":"test", "Node9":"test", "Pig":"test", "Rat":"test", "RhMonkey":"test" } }, "timers":{ "Baseline Fit":{ "order":1, "timer":88 }, "Overall":{ "order":0, "timer":121 }, "Residue A analysis":{ "order":2, "timer":2 }, "Residue C analysis":{ "order":3, "timer":1 }, "Residue D analysis":{ "order":4, "timer":1 }, "Residue E analysis":{ "order":5, "timer":1 }, "Residue F analysis":{ "order":6, "timer":2 }, "Residue G analysis":{ "order":7, "timer":1 }, "Residue H analysis":{ "order":8, "timer":2 }, "Residue I analysis":{ "order":9, "timer":1 }, "Residue K analysis":{ "order":10, "timer":2 }, "Residue L analysis":{ "order":11, "timer":1 }, "Residue M analysis":{ "order":12, "timer":2 }, "Residue N analysis":{ "order":13, "timer":2 }, "Residue P analysis":{ "order":14, "timer":1 }, "Residue Q analysis":{ "order":15, "timer":2 }, "Residue R analysis":{ "order":16, "timer":2 }, "Residue S analysis":{ "order":17, "timer":2 }, "Residue T analysis":{ "order":18, "timer":2 }, "Residue V analysis":{ "order":19, "timer":2 }, "Residue W analysis":{ "order":20, "timer":2 }, "Residue Y analysis":{ "order":21, "timer":2 } } }