Mercurial > repos > iuc > hyphy_conv

annotate test-data/busted-out2-1.json @ 9:3ea647006f17 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
author iuc
date Wed, 30 Mar 2022 00:16:40 +0000
parents 079ea2eb9ae4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
1 {
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
2 "Evidence Ratios":{
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
3 "constrained": [
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079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
diff changeset
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f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
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5 ],
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
6 "optimized null": [
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079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
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f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
8 ]
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
9 },
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
10 "Site Log Likelihood":{
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
11 "constrained": [
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079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
diff changeset
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f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
13 ],
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
14 "optimized null": [
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079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
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2
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
16 ],
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
17 "unconstrained": [
8
079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
diff changeset
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f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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parents:
diff changeset
19 ]
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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parents:
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20 },
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
21 "analysis":{
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
22 "authors":"Sergei L Kosakovsky Pond",
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
23 "citation":"*Gene-wide identification of episodic selection*, Mol Biol Evol. 32(5):1365-71",
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
24 "contact":"spond@temple.edu",
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
25 "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",
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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parents:
diff changeset
26 "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})",
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
27 "version":"3.1"
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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28 },
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079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
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parents: 2
diff changeset
29 "background":1,
2
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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parents:
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30 "branch attributes":{
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
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31 "0":{
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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32 "B_FR_83_HXB2":{
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079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
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parents: 2
diff changeset
33 "MG94xREV with separate rates for branch sets":0.0124534911696585,
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f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
34 "Nucleotide GTR":0.01178680392701259,
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079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
diff changeset
35 "constrained":0.0133332678009897,
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f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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36 "original name":"B_FR_83_HXB2",
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079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
diff changeset
37 "unconstrained":0.01333097793183841
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f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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38 },
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
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39 "B_US_83_RF":{
8
079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
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parents: 2
diff changeset
40 "MG94xREV with separate rates for branch sets":0.02861194347570897,
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f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
41 "Nucleotide GTR":0.02637179869727959,
8
079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
diff changeset
42 "constrained":0.03221962988361129,
2
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
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43 "original name":"B_US_83_RF",
8
079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
diff changeset
44 "unconstrained":0.03256468480049571
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f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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45 },
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
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46 "B_US_86_JRFL":{
8
079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
diff changeset
47 "MG94xREV with separate rates for branch sets":0.01907096200225401,
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f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
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48 "Nucleotide GTR":0.01766254318226218,
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079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
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parents: 2
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49 "constrained":0.0202680273768515,
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f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
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50 "original name":"B_US_86_JRFL",
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079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
diff changeset
51 "unconstrained":0.02050998211592096
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f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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52 },
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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parents:
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53 "B_US_90_WEAU160":{
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079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
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parents: 2
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54 "MG94xREV with separate rates for branch sets":0.0228124185259555,
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f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
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55 "Nucleotide GTR":0.0208836028381146,
8
079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
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56 "constrained":0.02350080060535386,
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f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
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57 "original name":"B_US_90_WEAU160",
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079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
diff changeset
58 "unconstrained":0.03169576721730974
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f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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59 },
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
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60 "D_CD_83_ELI":{
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079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
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parents: 2
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61 "MG94xREV with separate rates for branch sets":0.02096580136021227,
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iuc
parents:
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62 "Nucleotide GTR":0.01905599613120992,
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079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
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63 "constrained":0.02146725583386667,
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f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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64 "original name":"D_CD_83_ELI",
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079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
diff changeset
65 "unconstrained":0.02163106296740794
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f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
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66 },
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
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67 "D_CD_83_NDK":{
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079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
diff changeset
68 "MG94xREV with separate rates for branch sets":0.01029979658511127,
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iuc
parents:
diff changeset
69 "Nucleotide GTR":0.009776698714183414,
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079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
diff changeset
70 "constrained":0.01035332290986223,
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iuc
parents:
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71 "original name":"D_CD_83_NDK",
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079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
diff changeset
72 "unconstrained":0.01033266120816073
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73 },
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iuc
parents:
diff changeset
74 "D_CD_84_84ZR085":{
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iuc
parents: 2
diff changeset
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iuc
parents:
diff changeset
76 "Nucleotide GTR":0.02822254903672137,
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iuc
parents: 2
diff changeset
77 "constrained":0.03323755030380494,
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iuc
parents:
diff changeset
78 "original name":"D_CD_84_84ZR085",
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079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
diff changeset
79 "unconstrained":0.03361093648063813
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iuc
parents:
diff changeset
80 },
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iuc
parents:
diff changeset
81 "D_UG_94_94UG114":{
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iuc
parents: 2
diff changeset
82 "MG94xREV with separate rates for branch sets":0.05961647055090802,
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iuc
parents:
diff changeset
83 "Nucleotide GTR":0.05323070232023583,
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iuc
parents: 2
diff changeset
84 "constrained":0.06686538335493719,
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iuc
parents:
diff changeset
85 "original name":"D_UG_94_94UG114",
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079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
diff changeset
86 "unconstrained":0.06754551106553502
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iuc
parents:
diff changeset
87 },
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iuc
parents:
diff changeset
88 "Node1":{
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iuc
parents: 2
diff changeset
89 "MG94xREV with separate rates for branch sets":0.02629484580500255,
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iuc
parents:
diff changeset
90 "Nucleotide GTR":0.02355240508560319,
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iuc
parents: 2
diff changeset
91 "constrained":0.02886080451868769,
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iuc
parents: 2
diff changeset
92 "unconstrained":0.02913820563215103
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iuc
parents:
diff changeset
93 },
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iuc
parents:
diff changeset
94 "Node10":{
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iuc
parents: 2
diff changeset
95 "MG94xREV with separate rates for branch sets":0.001918758877996093,
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iuc
parents:
diff changeset
96 "Nucleotide GTR":0.002230248981703367,
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079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
diff changeset
97 "constrained":0.001805007516719466,
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iuc
parents: 2
diff changeset
98 "unconstrained":0.001821173275343402
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iuc
parents:
diff changeset
99 },
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iuc
parents:
diff changeset
100 "Node2":{
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iuc
parents: 2
diff changeset
101 "MG94xREV with separate rates for branch sets":0.003971092177388864,
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iuc
parents:
diff changeset
102 "Nucleotide GTR":0.003949360371801276,
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iuc
parents: 2
diff changeset
103 "constrained":0.002472638754288051,
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iuc
parents: 2
diff changeset
104 "unconstrained":0.002387715711685514
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iuc
parents:
diff changeset
105 },
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iuc
parents:
diff changeset
106 "Node3":{
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079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
diff changeset
107 "MG94xREV with separate rates for branch sets":0.01135514370835145,
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f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
108 "Nucleotide GTR":0.01048442975058683,
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079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
diff changeset
109 "constrained":0.01356000749275525,
079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
diff changeset
110 "unconstrained":0.01374972129226249
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f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
111 },
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
112 "Node9":{
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iuc
parents: 2
diff changeset
113 "MG94xREV with separate rates for branch sets":0.005568732807049801,
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iuc
parents:
diff changeset
114 "Nucleotide GTR":0.004986123424162501,
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079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
diff changeset
115 "constrained":0.00559084970119209,
079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
diff changeset
116 "unconstrained":0.005669013080318036
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iuc
parents:
diff changeset
117 }
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
118 },
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
119 "attributes":{
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
120 "MG94xREV with separate rates for branch sets":{
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iuc
parents:
diff changeset
121 "attribute type":"branch length",
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
122 "display order":1
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
123 },
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
124 "Nucleotide GTR":{
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iuc
parents:
diff changeset
125 "attribute type":"branch length",
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
126 "display order":0
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
127 },
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
128 "constrained":{
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iuc
parents:
diff changeset
129 "attribute type":"branch length",
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
130 "display order":1
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
131 },
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
132 "original name":{
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
133 "attribute type":"node label",
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
134 "display order":0
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
135 },
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
136 "unconstrained":{
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iuc
parents:
diff changeset
137 "attribute type":"branch length",
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
138 "display order":0
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
139 }
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
140 }
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
141 },
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
142 "data partitions":{
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
143 "0":{
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iuc
parents:
diff changeset
144 "coverage": [
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
145 [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, 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, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439]
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
146 ],
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
147 "name":"busted.filter.default"
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
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148 }
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
149 },
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
150 "fits":{
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iuc
parents:
diff changeset
151 "Constrained model":{
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079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
diff changeset
152 "AIC-c":6401.571605880178,
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iuc
parents: 2
diff changeset
153 "Log Likelihood":-3164.403373999521,
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iuc
parents:
diff changeset
154 "Rate Distributions":{
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079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
diff changeset
155 "Background":{
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iuc
parents: 2
diff changeset
156 "0":{
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iuc
parents: 2
diff changeset
157 "omega":0.1702532607798455,
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iuc
parents: 2
diff changeset
158 "proportion":0.8127334552706815
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iuc
parents: 2
diff changeset
159 },
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iuc
parents: 2
diff changeset
160 "1":{
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iuc
parents: 2
diff changeset
161 "omega":0.2017838473060485,
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iuc
parents: 2
diff changeset
162 "proportion":0.1774848965120759
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iuc
parents: 2
diff changeset
163 },
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iuc
parents: 2
diff changeset
164 "2":{
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iuc
parents: 2
diff changeset
165 "omega":13.15236788524238,
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iuc
parents: 2
diff changeset
166 "proportion":0.00978164821724258
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iuc
parents: 2
diff changeset
167 }
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iuc
parents: 2
diff changeset
168 },
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iuc
parents:
diff changeset
169 "Test":{
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iuc
parents:
diff changeset
170 "0":{
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iuc
parents:
diff changeset
171 "omega":0,
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iuc
parents: 2
diff changeset
172 "proportion":0.8358903801628909
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iuc
parents:
diff changeset
173 },
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iuc
parents:
diff changeset
174 "1":{
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079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
diff changeset
175 "omega":1,
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iuc
parents: 2
diff changeset
176 "proportion":0.1436055877954064
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iuc
parents:
diff changeset
177 },
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iuc
parents:
diff changeset
178 "2":{
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iuc
parents:
diff changeset
179 "omega":1,
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079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
diff changeset
180 "proportion":0.02050403204170275
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iuc
parents:
diff changeset
181 }
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iuc
parents:
diff changeset
182 }
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iuc
parents:
diff changeset
183 },
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iuc
parents:
diff changeset
184 "display order":3,
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079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
diff changeset
185 "estimated parameters":36
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iuc
parents:
diff changeset
186 },
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iuc
parents:
diff changeset
187 "MG94xREV with separate rates for branch sets":{
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079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
diff changeset
188 "AIC-c":6410.490466219016,
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iuc
parents:
diff changeset
189 "Equilibrium frequencies": [
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iuc
parents:
diff changeset
190 [0.07535940345366139],
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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iuc
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diff changeset
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iuc
parents:
diff changeset
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iuc
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diff changeset
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iuc
parents:
diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
parents:
diff changeset
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iuc
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diff changeset
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iuc
parents:
diff changeset
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iuc
parents:
diff changeset
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iuc
parents:
diff changeset
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iuc
parents:
diff changeset
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iuc
parents:
diff changeset
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iuc
parents:
diff changeset
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iuc
parents:
diff changeset
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iuc
parents:
diff changeset
215 [0.002882972930821469],
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iuc
parents:
diff changeset
216 [0.005825499564956559],
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iuc
parents:
diff changeset
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iuc
parents:
diff changeset
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iuc
parents:
diff changeset
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iuc
parents:
diff changeset
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iuc
parents:
diff changeset
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iuc
parents:
diff changeset
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iuc
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diff changeset
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iuc
parents:
diff changeset
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iuc
parents:
diff changeset
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iuc
parents:
diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
parents:
diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
235 [0.006527245376826684],
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iuc
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diff changeset
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iuc
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diff changeset
237 [0.01336595951511979],
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
244 [0.004328407393735399],
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iuc
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diff changeset
245 [0.008746226896405704],
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iuc
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diff changeset
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iuc
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diff changeset
247 [0.03414665788893068],
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iuc
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diff changeset
248 [0.006538513303760755],
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iuc
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diff changeset
249 [0.0132120929750345],
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iuc
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diff changeset
250 [0.01338903305480236]
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iuc
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diff changeset
251 ],
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iuc
parents: 2
diff changeset
252 "Log Likelihood":-3175.995949441886,
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iuc
parents:
diff changeset
253 "Rate Distributions":{
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iuc
parents: 2
diff changeset
254 "non-synonymous/synonymous rate ratio for *background*": [
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iuc
parents: 2
diff changeset
255 [0.2379324068936849, 1]
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iuc
parents: 2
diff changeset
256 ],
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iuc
parents:
diff changeset
257 "non-synonymous/synonymous rate ratio for *test*": [
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iuc
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diff changeset
258 [0.1777604776475358, 1]
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iuc
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diff changeset
259 ]
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iuc
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diff changeset
260 },
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iuc
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diff changeset
261 "display order":1,
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iuc
parents: 2
diff changeset
262 "estimated parameters":29
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iuc
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diff changeset
263 },
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iuc
parents:
diff changeset
264 "Nucleotide GTR":{
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iuc
parents:
diff changeset
265 "AIC-c":6683.094244259512,
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iuc
parents:
diff changeset
266 "Equilibrium frequencies": [
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iuc
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diff changeset
267 [0.4044507575757576],
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iuc
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diff changeset
268 [0.1662878787878788],
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iuc
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diff changeset
269 [0.2095643939393939],
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iuc
parents:
diff changeset
270 [0.2196969696969697]
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iuc
parents:
diff changeset
271 ],
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iuc
parents:
diff changeset
272 "Log Likelihood":-3320.503280793639,
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iuc
parents:
diff changeset
273 "Rate Distributions":{
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iuc
parents:
diff changeset
274 "Substitution rate from nucleotide A to nucleotide C":0.1815218119292989,
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iuc
parents:
diff changeset
275 "Substitution rate from nucleotide A to nucleotide G":1,
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iuc
parents:
diff changeset
276 "Substitution rate from nucleotide A to nucleotide T":0.08433479296165451,
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iuc
parents:
diff changeset
277 "Substitution rate from nucleotide C to nucleotide G":0.1775869374255926,
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iuc
parents:
diff changeset
278 "Substitution rate from nucleotide C to nucleotide T":1.184827038118431,
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iuc
parents:
diff changeset
279 "Substitution rate from nucleotide G to nucleotide T":0.04288318031815568
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iuc
parents:
diff changeset
280 },
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iuc
parents:
diff changeset
281 "display order":0,
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iuc
parents:
diff changeset
282 "estimated parameters":21
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iuc
parents:
diff changeset
283 },
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iuc
parents:
diff changeset
284 "Unconstrained model":{
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iuc
parents: 2
diff changeset
285 "AIC-c":6400.149223170942,
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iuc
parents: 2
diff changeset
286 "Log Likelihood":-3162.670820660715,
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iuc
parents:
diff changeset
287 "Rate Distributions":{
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iuc
parents: 2
diff changeset
288 "Background":{
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iuc
parents: 2
diff changeset
289 "0":{
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iuc
parents: 2
diff changeset
290 "omega":0.1679188282558003,
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iuc
parents: 2
diff changeset
291 "proportion":0.8207520434237199
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iuc
parents: 2
diff changeset
292 },
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iuc
parents: 2
diff changeset
293 "1":{
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iuc
parents: 2
diff changeset
294 "omega":0.2120937673953722,
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iuc
parents: 2
diff changeset
295 "proportion":0.1693698006934513
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iuc
parents: 2
diff changeset
296 },
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iuc
parents: 2
diff changeset
297 "2":{
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iuc
parents: 2
diff changeset
298 "omega":13.84252711122189,
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iuc
parents: 2
diff changeset
299 "proportion":0.00987815588282877
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iuc
parents: 2
diff changeset
300 }
079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
diff changeset
301 },
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iuc
parents:
diff changeset
302 "Test":{
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iuc
parents:
diff changeset
303 "0":{
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iuc
parents: 2
diff changeset
304 "omega":0.08367159828032572,
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iuc
parents: 2
diff changeset
305 "proportion":0.9533274940567786
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f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
306 },
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
307 "1":{
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iuc
parents: 2
diff changeset
308 "omega":0.2493792697064242,
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iuc
parents: 2
diff changeset
309 "proportion":0.03716922067476962
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f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
310 },
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iuc
parents:
diff changeset
311 "2":{
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iuc
parents: 2
diff changeset
312 "omega":34.20463703717275,
079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
diff changeset
313 "proportion":0.009503285268451747
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f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
314 }
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
315 }
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
316 },
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
317 "display order":2,
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079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
diff changeset
318 "estimated parameters":37
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f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
319 }
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
320 },
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
diff changeset
321 "input":{
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079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
diff changeset
322 "file name":"/tmp/tmpfzf3u9m4/job_working_directory/000/2/working/./input.nex",
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iuc
parents:
diff changeset
323 "number of sequences":8,
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iuc
parents:
diff changeset
324 "number of sites":440,
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
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325 "partition count":1,
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
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326 "trees":{
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
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327 "0":"((((D_CD_83_ELI,D_CD_83_NDK)Node3,D_UG_94_94UG114)Node2,D_CD_84_84ZR085)Node1,B_US_83_RF,((B_FR_83_HXB2,B_US_86_JRFL)Node10,B_US_90_WEAU160)Node9)"
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
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328 }
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
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329 },
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
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330 "test results":{
8
079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
diff changeset
331 "LRT":3.465106677611402,
079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
diff changeset
332 "p-value":0.08841616008911996
2
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
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333 },
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
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334 "tested":{
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
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335 "0":{
8
079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
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336 "B_FR_83_HXB2":"background",
079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
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337 "B_US_83_RF":"background",
079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
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338 "B_US_86_JRFL":"background",
2
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
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339 "B_US_90_WEAU160":"test",
8
079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
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340 "D_CD_83_ELI":"background",
079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
diff changeset
341 "D_CD_83_NDK":"background",
079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
diff changeset
342 "D_CD_84_84ZR085":"background",
079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
diff changeset
343 "D_UG_94_94UG114":"background",
079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
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344 "Node1":"background",
079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
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345 "Node10":"background",
079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
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346 "Node2":"background",
079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
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347 "Node3":"background",
079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
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348 "Node9":"background"
2
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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parents:
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349 }
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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parents:
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350 },
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
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351 "timers":{
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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parents:
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352 "Constrained BUSTED model fitting":{
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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parents:
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353 "order":3,
8
079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
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parents: 2
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354 "timer":14
2
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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355 },
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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356 "Overall":{
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
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357 "order":0,
8
079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
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parents: 2
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358 "timer":60
2
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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parents:
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359 },
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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parents:
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360 "Preliminary model fitting":{
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
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361 "order":1,
8
079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
iuc
parents: 2
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362 "timer":3
2
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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parents:
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363 },
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
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364 "Unconstrained BUSTED model fitting":{
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents:
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365 "order":2,
8
079ea2eb9ae4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e74f0c1ed183da674db365c3a6ce320b0c08d9bc"
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parents: 2
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366 "timer":40
2
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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367 }
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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parents:
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368 }
f6e7b5955712 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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369 }