Mercurial > repos > iuc > hyphy_bgm

annotate test-data/busted-out1.json @ 21:df8c64576038 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d44a94772c58903157edfc12c2a67819cfe252a9"
author iuc
date Wed, 24 Feb 2021 19:03:58 +0000
parents cdfa1afd7cb0
children d88bbb287923
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rev   line source
0
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
1 {
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cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
iuc
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diff changeset
2 "Evidence Ratios":{
cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
iuc
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diff changeset
3 "constrained": [
cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
iuc
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diff changeset
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cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
iuc
parents: 0
diff changeset
5 ],
cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
iuc
parents: 0
diff changeset
6 "optimized null": [
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iuc
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diff changeset
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cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
iuc
parents: 0
diff changeset
8 ]
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bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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parents:
diff changeset
9 },
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cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
iuc
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10 "Site Log Likelihood":{
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iuc
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diff changeset
11 "constrained": [
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iuc
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diff changeset
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cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
iuc
parents: 0
diff changeset
13 ],
cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
iuc
parents: 0
diff changeset
14 "optimized null": [
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iuc
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cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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diff changeset
17 "unconstrained": [
cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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20 },
cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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diff changeset
21 "Synonymous site-posteriors": [
cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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25 ],
cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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26 "analysis":{
cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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27 "authors":"Sergei L Kosakovsky Pond",
cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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diff changeset
28 "citation":"*Gene-wide identification of episodic selection*, Mol Biol Evol. 32(5):1365-71",
cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
iuc
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diff changeset
29 "contact":"spond@temple.edu",
cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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diff changeset
30 "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\n",
cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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diff changeset
31 "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})",
cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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diff changeset
32 "version":"3.0"
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bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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diff changeset
33 },
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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34 "background":0,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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35 "branch attributes":{
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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36 "0":{
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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37 "Baboon":{
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cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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38 "MG94xREV with separate rates for branch sets":0.001771850913718116,
cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
iuc
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diff changeset
39 "Nucleotide GTR":0.00167976779100812,
cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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40 "constrained":0.0005055252388761481,
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bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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diff changeset
41 "original name":"Baboon",
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42 "unconstrained":0.0005398732671668005
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43 },
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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44 "Cat":{
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cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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45 "MG94xREV with separate rates for branch sets":0.2738959056554072,
cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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46 "Nucleotide GTR":0.266075486389923,
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47 "constrained":0.1152712488116292,
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diff changeset
48 "original name":"Cat",
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cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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49 "unconstrained":0.120218071527276
cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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50 },
cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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diff changeset
51 "Chimp":{
cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
iuc
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diff changeset
52 "MG94xREV with separate rates for branch sets":0.001827968855137289,
cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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diff changeset
53 "Nucleotide GTR":0.001817801565830578,
cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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diff changeset
54 "constrained":0.0006181497274348637,
cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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diff changeset
55 "original name":"Chimp",
cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
iuc
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diff changeset
56 "unconstrained":0.0006183542388399873
cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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diff changeset
57 },
cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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diff changeset
58 "Cow":{
cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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diff changeset
59 "MG94xREV with separate rates for branch sets":0.2477119781238836,
cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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diff changeset
60 "Nucleotide GTR":0.2480176045457076,
cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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diff changeset
61 "constrained":0.1036665344622347,
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diff changeset
62 "original name":"Cow",
cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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diff changeset
63 "unconstrained":0.1088268022245659
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64 },
cdfa1afd7cb0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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diff changeset
65 "Horse":{
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diff changeset
66 "MG94xREV with separate rates for branch sets":0.211203801568566,
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diff changeset
67 "Nucleotide GTR":0.2090856782081004,
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157 "original name":{
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158 "attribute type":"node label",
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178 "Log Likelihood":-3419.573452280089,
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179 "Rate Distributions":{
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180 "Synonymous site-to-site rates":{
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194 "Test":{
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203 "2":{
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209 "display order":3,
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210 "estimated parameters":39
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212 "MG94xREV with separate rates for branch sets":{
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213 "AIC-c":6997.089050462658,
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214 "Equilibrium frequencies": [
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277 "Log Likelihood":-3467.004808147542,
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278 "Rate Distributions":{
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279 "non-synonymous/synonymous rate ratio for *test*": [
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280 [0.9950576192409499, 1]
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281 ]
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282 },
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283 "display order":1,
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284 "estimated parameters":31
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285 },
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286 "Nucleotide GTR":{
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287 "AIC-c":7112.85745601076,
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288 "Equilibrium frequencies": [
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293 ],
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294 "Log Likelihood":-3532.321297387654,
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295 "Rate Distributions":{
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296 "Substitution rate from nucleotide A to nucleotide C":0.5497129763145497,
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297 "Substitution rate from nucleotide A to nucleotide G":1,
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298 "Substitution rate from nucleotide A to nucleotide T":0.264666902964203,
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299 "Substitution rate from nucleotide C to nucleotide G":0.4916303643305098,
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300 "Substitution rate from nucleotide C to nucleotide T":1.027924764411573,
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301 "Substitution rate from nucleotide G to nucleotide T":0.304615404570875
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302 },
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303 "display order":0,
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304 "estimated parameters":24
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305 },
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306 "Unconstrained model":{
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307 "AIC-c":6910.766610587704,
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308 "Log Likelihood":-3414.486640449675,
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309 "Rate Distributions":{
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310 "Synonymous site-to-site rates":{
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311 "0":{
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312 "proportion":0.2645541257391169,
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313 "rate":0.2747941124675511
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314 },
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315 "1":{
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316 "proportion":0.6325830460054784,
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317 "rate":0.9734675888351726
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318 },
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319 "2":{
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320 "proportion":0.1028628282554047,
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321 "rate":3.028333913894314
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322 }
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323 },
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324 "Test":{
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325 "0":{
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327 "proportion":0.04809457608200497
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328 },
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330 "omega":0,
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331 "proportion":0.3410012743721951
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332 },
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333 "2":{
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334 "omega":1.89363684081788,
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335 "proportion":0.6109041495458
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338 },
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339 "display order":2,
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340 "estimated parameters":40
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341 }
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342 },
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343 "input":{
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344 "file name":"/tmp/tmp7qHfo2/job_working_directory/000/3/working/./busted_input.fa",
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345 "number of sequences":10,
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346 "number of sites":187,
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347 "partition count":1,
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348 "trees":{
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349 "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)"
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351 },
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352 "test results":{
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353 "LRT":10.17362366082671,
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354 "p-value":0.003088842014430382
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355 },
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356 "tested":{
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357 "0":{
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358 "Baboon":"test",
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359 "Cat":"test",
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360 "Chimp":"test",
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361 "Cow":"test",
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362 "Horse":"test",
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363 "Human":"test",
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364 "Mouse":"test",
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365 "Node1":"test",
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366 "Node12":"test",
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367 "Node2":"test",
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368 "Node3":"test",
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369 "Node8":"test",
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370 "Node9":"test",
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371 "Pig":"test",
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372 "Rat":"test",
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373 "RhMonkey":"test"
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374 }
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375 },
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376 "timers":{
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377 "Constrained BUSTED model fitting":{
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378 "order":3,
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379 "timer":62
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380 },
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381 "Overall":{
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382 "order":0,
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383 "timer":228
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384 },
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385 "Preliminary model fitting":{
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386 "order":1,
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387 "timer":3
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388 },
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389 "Unconstrained BUSTED model fitting":{
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390 "order":2,
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391 "timer":161
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392 }
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394 }