Mercurial > repos > iuc > hyphy_relax

annotate test-data/absrel-out2.json @ 32:49885a825dc1 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 00:12:50 +0000
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32
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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1 {
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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2 "Synonymous site-posteriors": [
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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diff changeset
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49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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6 ],
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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7 "analysis":{
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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8 "authors":"Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution group",
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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9 "citation":"Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection (2015). Mol Biol Evol 32 (5): 1342-1353. v2.2 adds support for multiple-hit models. v2.3 adds support for SRV",
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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10 "contact":"spond@temple.edu",
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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11 "info":"aBSREL (Adaptive branch-site random effects likelihood)\n uses an adaptive random effects branch-site model framework\n to test whether each branch has evolved under positive selection,\n using a procedure which infers an optimal number of rate categories per branch.",
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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12 "requirements":"in-frame codon alignment and a phylogenetic tree",
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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13 "version":"2.3"
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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14 },
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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15 "branch attributes":{
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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16 "0":{
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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17 "Baboon":{
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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18 "Baseline MG94xREV":0.001882994109917251,
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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19 "Baseline MG94xREV omega ratio":0,
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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20 "Corrected P-value":1,
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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21 "Full adaptive model":0.001888788495524889,
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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22 "Full adaptive model (non-synonymous subs/site)":1e-10,
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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23 "Full adaptive model (synonymous subs/site)":0.001888788495524889,
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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24 "LRT":0,
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
25 "Nucleotide GTR":0.001685167654714891,
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iuc
parents:
diff changeset
26 "Rate Distributions": [
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iuc
parents:
diff changeset
27 [0, 1]
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iuc
parents:
diff changeset
28 ],
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
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diff changeset
29 "Rate classes":1,
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iuc
parents:
diff changeset
30 "Uncorrected P-value":1,
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iuc
parents:
diff changeset
31 "original name":"Baboon",
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iuc
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diff changeset
32 "rate at which 2 nucleotides are changed instantly within a single codon":0
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iuc
parents:
diff changeset
33 },
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iuc
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diff changeset
34 "Cat":{
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iuc
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diff changeset
35 "Baseline MG94xREV":0.2956038491638456,
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iuc
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diff changeset
36 "Baseline MG94xREV omega ratio":1.387276691142692,
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iuc
parents:
diff changeset
37 "Corrected P-value":1,
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iuc
parents:
diff changeset
38 "Full adaptive model":0.2987657142024844,
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iuc
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diff changeset
39 "Full adaptive model (non-synonymous subs/site)":0.2433925676712428,
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iuc
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diff changeset
40 "Full adaptive model (synonymous subs/site)":0.05537314653124186,
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iuc
parents:
diff changeset
41 "LRT":0.8385257143854687,
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iuc
parents:
diff changeset
42 "Nucleotide GTR":0.2660536011315811,
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iuc
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diff changeset
43 "Rate Distributions": [
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iuc
parents:
diff changeset
44 [1.406509052931997, 1]
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iuc
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diff changeset
45 ],
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iuc
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diff changeset
46 "Rate classes":1,
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iuc
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diff changeset
47 "Uncorrected P-value":0.2692231522977311,
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iuc
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diff changeset
48 "original name":"Cat",
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iuc
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diff changeset
49 "rate at which 2 nucleotides are changed instantly within a single codon":0.2039176940606485
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iuc
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diff changeset
50 },
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iuc
parents:
diff changeset
51 "Chimp":{
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iuc
parents:
diff changeset
52 "Baseline MG94xREV":0.001849682046955941,
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iuc
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diff changeset
53 "Baseline MG94xREV omega ratio":10000000000,
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iuc
parents:
diff changeset
54 "Corrected P-value":1,
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iuc
parents:
diff changeset
55 "Full adaptive model":0.001852710195778403,
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iuc
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diff changeset
56 "Full adaptive model (non-synonymous subs/site)":0.001852710195778403,
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iuc
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diff changeset
57 "Full adaptive model (synonymous subs/site)":1e-10,
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iuc
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diff changeset
58 "LRT":0.6095489899789754,
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iuc
parents:
diff changeset
59 "Nucleotide GTR":0.001820258053351119,
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iuc
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diff changeset
60 "Rate Distributions": [
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iuc
parents:
diff changeset
61 [10000000000, 1]
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iuc
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diff changeset
62 ],
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iuc
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diff changeset
63 "Rate classes":1,
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iuc
parents:
diff changeset
64 "Uncorrected P-value":0.3081784202350423,
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iuc
parents:
diff changeset
65 "original name":"Chimp",
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iuc
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diff changeset
66 "rate at which 2 nucleotides are changed instantly within a single codon":0
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iuc
parents:
diff changeset
67 },
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iuc
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diff changeset
68 "Cow":{
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iuc
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diff changeset
69 "Baseline MG94xREV":0.2725380828787176,
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iuc
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diff changeset
70 "Baseline MG94xREV omega ratio":1.996288552263199,
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iuc
parents:
diff changeset
71 "Corrected P-value":1,
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iuc
parents:
diff changeset
72 "Full adaptive model":0.2767543531983568,
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iuc
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diff changeset
73 "Full adaptive model (non-synonymous subs/site)":0.2381665266426745,
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iuc
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diff changeset
74 "Full adaptive model (synonymous subs/site)":0.03858782655568219,
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iuc
parents:
diff changeset
75 "LRT":3.11056227267909,
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iuc
parents:
diff changeset
76 "Nucleotide GTR":0.2480198736772598,
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iuc
parents:
diff changeset
77 "Rate Distributions": [
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iuc
parents:
diff changeset
78 [2.042233367641365, 1]
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iuc
parents:
diff changeset
79 ],
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iuc
parents:
diff changeset
80 "Rate classes":1,
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iuc
parents:
diff changeset
81 "Uncorrected P-value":0.07889622593515888,
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iuc
parents:
diff changeset
82 "original name":"Cow",
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iuc
parents:
diff changeset
83 "rate at which 2 nucleotides are changed instantly within a single codon":0.1380461206420348
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iuc
parents:
diff changeset
84 },
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iuc
parents:
diff changeset
85 "Horse":{
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iuc
parents:
diff changeset
86 "Baseline MG94xREV":0.2306806115249962,
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iuc
parents:
diff changeset
87 "Baseline MG94xREV omega ratio":1.164040491954013,
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iuc
parents:
diff changeset
88 "Corrected P-value":1,
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iuc
parents:
diff changeset
89 "Full adaptive model":0.2320795562671627,
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iuc
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diff changeset
90 "Full adaptive model (non-synonymous subs/site)":0.1780556222700155,
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iuc
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diff changeset
91 "Full adaptive model (synonymous subs/site)":0.05402393399714727,
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iuc
parents:
diff changeset
92 "LRT":0.2293786685804662,
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iuc
parents:
diff changeset
93 "Nucleotide GTR":0.2090998951755368,
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iuc
parents:
diff changeset
94 "Rate Distributions": [
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iuc
parents:
diff changeset
95 [1.174701177865617, 1]
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iuc
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diff changeset
96 ],
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iuc
parents:
diff changeset
97 "Rate classes":1,
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iuc
parents:
diff changeset
98 "Uncorrected P-value":0.393889915055757,
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iuc
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diff changeset
99 "original name":"Horse",
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iuc
parents:
diff changeset
100 "rate at which 2 nucleotides are changed instantly within a single codon":0
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iuc
parents:
diff changeset
101 },
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iuc
parents:
diff changeset
102 "Human":{
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iuc
parents:
diff changeset
103 "Baseline MG94xREV":0,
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iuc
parents:
diff changeset
104 "Baseline MG94xREV omega ratio":1,
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iuc
parents:
diff changeset
105 "Corrected P-value":1,
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iuc
parents:
diff changeset
106 "Full adaptive model":0,
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iuc
parents:
diff changeset
107 "Full adaptive model (non-synonymous subs/site)":1e-10,
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iuc
parents:
diff changeset
108 "Full adaptive model (synonymous subs/site)":1e-10,
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iuc
parents:
diff changeset
109 "LRT":0,
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iuc
parents:
diff changeset
110 "Nucleotide GTR":0,
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iuc
parents:
diff changeset
111 "Rate Distributions": [
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iuc
parents:
diff changeset
112 [1, 1]
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iuc
parents:
diff changeset
113 ],
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
114 "Rate classes":1,
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iuc
parents:
diff changeset
115 "Uncorrected P-value":1,
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iuc
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diff changeset
116 "original name":"Human",
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iuc
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diff changeset
117 "rate at which 2 nucleotides are changed instantly within a single codon":0.0009494209875164728
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iuc
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diff changeset
118 },
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iuc
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diff changeset
119 "Mouse":{
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iuc
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diff changeset
120 "Baseline MG94xREV":0.130389131191465,
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iuc
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diff changeset
121 "Baseline MG94xREV omega ratio":0.5075430486034895,
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iuc
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diff changeset
122 "Corrected P-value":1,
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iuc
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diff changeset
123 "Full adaptive model":0.1314019024803463,
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iuc
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diff changeset
124 "Full adaptive model (non-synonymous subs/site)":0.07806862630983659,
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diff changeset
125 "Full adaptive model (synonymous subs/site)":0.05333327617050967,
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iuc
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diff changeset
126 "LRT":0,
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iuc
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diff changeset
127 "Nucleotide GTR":0.1181058300538561,
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iuc
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diff changeset
128 "Rate Distributions": [
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diff changeset
129 [0.5153237391744061, 1]
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diff changeset
130 ],
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diff changeset
131 "Rate classes":1,
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diff changeset
132 "Uncorrected P-value":1,
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diff changeset
133 "original name":"Mouse",
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diff changeset
134 "rate at which 2 nucleotides are changed instantly within a single codon":0.02214869577417109
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diff changeset
135 },
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diff changeset
136 "Node1":{
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diff changeset
137 "Baseline MG94xREV":0.3335904378274563,
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diff changeset
138 "Baseline MG94xREV omega ratio":0.296025779706705,
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diff changeset
139 "Corrected P-value":1,
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diff changeset
140 "Full adaptive model":0.3367504162367471,
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diff changeset
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diff changeset
142 "Full adaptive model (synonymous subs/site)":0.1643358193865155,
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diff changeset
143 "LRT":0,
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iuc
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diff changeset
144 "Nucleotide GTR":0.2767105173979571,
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diff changeset
145 "Rate Distributions": [
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diff changeset
146 [0.3015051917009056, 1]
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diff changeset
147 ],
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diff changeset
148 "Rate classes":1,
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iuc
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diff changeset
149 "Uncorrected P-value":1,
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diff changeset
150 "rate at which 2 nucleotides are changed instantly within a single codon":0.4322434210228028
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diff changeset
151 },
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diff changeset
152 "Node12":{
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diff changeset
153 "Baseline MG94xREV":0.01392429623408649,
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diff changeset
154 "Baseline MG94xREV omega ratio":0.2780699887855826,
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iuc
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diff changeset
155 "Corrected P-value":1,
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diff changeset
156 "Full adaptive model":0.01389906280188583,
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diff changeset
157 "Full adaptive model (non-synonymous subs/site)":0.006925004412300655,
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diff changeset
158 "Full adaptive model (synonymous subs/site)":0.006974058389585205,
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diff changeset
159 "LRT":0,
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iuc
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diff changeset
160 "Nucleotide GTR":0.01784222107494562,
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iuc
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diff changeset
161 "Rate Distributions": [
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iuc
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diff changeset
162 [0.2813759516294281, 1]
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diff changeset
163 ],
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diff changeset
164 "Rate classes":1,
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iuc
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diff changeset
165 "Uncorrected P-value":1,
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diff changeset
166 "rate at which 2 nucleotides are changed instantly within a single codon":0.4640974620285408
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diff changeset
167 },
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iuc
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diff changeset
168 "Node2":{
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diff changeset
169 "Baseline MG94xREV":0.04571805957848055,
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iuc
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diff changeset
170 "Baseline MG94xREV omega ratio":0.07808093503260165,
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iuc
parents:
diff changeset
171 "Corrected P-value":1,
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iuc
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diff changeset
172 "Full adaptive model":0.0459318071864371,
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diff changeset
173 "Full adaptive model (non-synonymous subs/site)":0.02632650948831447,
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diff changeset
174 "Full adaptive model (synonymous subs/site)":0.01960529769812262,
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iuc
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diff changeset
175 "LRT":0,
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iuc
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diff changeset
176 "Nucleotide GTR":0.06614755778044307,
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iuc
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diff changeset
177 "Rate Distributions": [
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iuc
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diff changeset
178 [0.07994399997950775, 1]
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diff changeset
179 ],
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iuc
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diff changeset
180 "Rate classes":1,
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iuc
parents:
diff changeset
181 "Uncorrected P-value":1,
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diff changeset
182 "rate at which 2 nucleotides are changed instantly within a single codon":10.77888358494443
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iuc
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diff changeset
183 },
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iuc
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diff changeset
184 "Node3":{
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diff changeset
185 "Baseline MG94xREV":0.1076878090259787,
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iuc
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diff changeset
186 "Baseline MG94xREV omega ratio":1.418168092305362,
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iuc
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diff changeset
187 "Corrected P-value":1,
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iuc
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diff changeset
188 "Full adaptive model":0.1082923487440297,
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diff changeset
189 "Full adaptive model (non-synonymous subs/site)":0.08948990966777266,
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diff changeset
190 "Full adaptive model (synonymous subs/site)":0.01880243907625684,
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iuc
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diff changeset
191 "LRT":0.2456529644996408,
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iuc
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diff changeset
192 "Nucleotide GTR":0.09883748387954429,
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iuc
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diff changeset
193 "Rate Distributions": [
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iuc
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diff changeset
194 [1.433858907010162, 1]
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diff changeset
195 ],
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diff changeset
196 "Rate classes":1,
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iuc
parents:
diff changeset
197 "Uncorrected P-value":0.389355679288724,
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iuc
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diff changeset
198 "rate at which 2 nucleotides are changed instantly within a single codon":0.3287265444712935
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diff changeset
199 },
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iuc
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diff changeset
200 "Node8":{
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iuc
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diff changeset
201 "Baseline MG94xREV":0.1135770124969486,
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iuc
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diff changeset
202 "Baseline MG94xREV omega ratio":2.028136557891868,
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iuc
parents:
diff changeset
203 "Corrected P-value":1,
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iuc
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diff changeset
204 "Full adaptive model":0.1147398059647541,
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diff changeset
205 "Full adaptive model (non-synonymous subs/site)":0.0990475665351926,
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diff changeset
206 "Full adaptive model (synonymous subs/site)":0.01569223942956148,
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diff changeset
207 "LRT":0.7886998749927443,
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iuc
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diff changeset
208 "Nucleotide GTR":0.1062201244057951,
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iuc
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diff changeset
209 "Rate Distributions": [
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diff changeset
210 [1.988476719481082, 1]
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diff changeset
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diff changeset
212 "Rate classes":1,
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diff changeset
213 "Uncorrected P-value":0.2771341436242022,
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diff changeset
214 "rate at which 2 nucleotides are changed instantly within a single codon":0.2354207827705045
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diff changeset
215 },
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diff changeset
216 "Node9":{
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diff changeset
217 "Baseline MG94xREV":0.03003888198106763,
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diff changeset
218 "Baseline MG94xREV omega ratio":0.4077675922423373,
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diff changeset
219 "Corrected P-value":1,
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iuc
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diff changeset
220 "Full adaptive model":0.03019973043687331,
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diff changeset
221 "Full adaptive model (non-synonymous subs/site)":0.01619043357790366,
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222 "Full adaptive model (synonymous subs/site)":0.01400929685896962,
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iuc
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diff changeset
223 "LRT":0,
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iuc
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diff changeset
224 "Nucleotide GTR":0.02567813733543303,
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iuc
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diff changeset
225 "Rate Distributions": [
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diff changeset
226 [0.4119078417573153, 1]
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diff changeset
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diff changeset
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229 "Uncorrected P-value":1,
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diff changeset
230 "rate at which 2 nucleotides are changed instantly within a single codon":0
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diff changeset
231 },
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diff changeset
232 "Pig":{
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diff changeset
233 "Baseline MG94xREV":0.217114312357174,
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iuc
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diff changeset
234 "Baseline MG94xREV omega ratio":1.283370430439691,
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diff changeset
235 "Corrected P-value":1,
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diff changeset
236 "Full adaptive model":0.2181331361104026,
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diff changeset
237 "Full adaptive model (non-synonymous subs/site)":0.1712686263446052,
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238 "Full adaptive model (synonymous subs/site)":0.04686450976579729,
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iuc
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diff changeset
239 "LRT":0.5406119303397645,
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iuc
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diff changeset
240 "Nucleotide GTR":0.1871390433004313,
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diff changeset
241 "Rate Distributions": [
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diff changeset
242 [1.302541757406645, 1]
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diff changeset
243 ],
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diff changeset
244 "Rate classes":1,
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iuc
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diff changeset
245 "Uncorrected P-value":0.3213796354214938,
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iuc
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diff changeset
246 "original name":"Pig",
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diff changeset
247 "rate at which 2 nucleotides are changed instantly within a single codon":0
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diff changeset
248 },
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iuc
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diff changeset
249 "Rat":{
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diff changeset
250 "Baseline MG94xREV":0.06785652890791004,
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diff changeset
251 "Baseline MG94xREV omega ratio":0.9234518387715737,
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iuc
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diff changeset
252 "Corrected P-value":1,
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iuc
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diff changeset
253 "Full adaptive model":0.06783877994658692,
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diff changeset
254 "Full adaptive model (non-synonymous subs/site)":0.04934287026354431,
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diff changeset
255 "Full adaptive model (synonymous subs/site)":0.01849590968304254,
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iuc
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diff changeset
256 "LRT":0,
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iuc
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diff changeset
257 "Nucleotide GTR":0.06661490534189227,
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diff changeset
258 "Rate Distributions": [
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diff changeset
259 [0.939079296251313, 1]
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diff changeset
260 ],
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iuc
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diff changeset
261 "Rate classes":1,
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iuc
parents:
diff changeset
262 "Uncorrected P-value":1,
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iuc
parents:
diff changeset
263 "original name":"Rat",
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iuc
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diff changeset
264 "rate at which 2 nucleotides are changed instantly within a single codon":0.02234985038534893
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diff changeset
265 },
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iuc
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diff changeset
266 "RhMonkey":{
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diff changeset
267 "Baseline MG94xREV":0.0036869629402653,
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iuc
parents:
diff changeset
268 "Baseline MG94xREV omega ratio":10000000000,
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iuc
parents:
diff changeset
269 "Corrected P-value":1,
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iuc
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diff changeset
270 "Full adaptive model":0.003691831254195047,
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iuc
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diff changeset
271 "Full adaptive model (non-synonymous subs/site)":0.003691831254195047,
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iuc
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diff changeset
272 "Full adaptive model (synonymous subs/site)":1e-10,
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iuc
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diff changeset
273 "LRT":1.049935795353122,
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iuc
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diff changeset
274 "Nucleotide GTR":0.003778804730491441,
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iuc
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diff changeset
275 "Rate Distributions": [
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iuc
parents:
diff changeset
276 [10000000000, 1]
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diff changeset
277 ],
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iuc
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diff changeset
278 "Rate classes":1,
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iuc
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diff changeset
279 "Uncorrected P-value":0.2385766813428075,
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iuc
parents:
diff changeset
280 "original name":"RhMonkey",
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iuc
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diff changeset
281 "rate at which 2 nucleotides are changed instantly within a single codon":0
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iuc
parents:
diff changeset
282 }
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parents:
diff changeset
283 },
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iuc
parents:
diff changeset
284 "attributes":{
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diff changeset
285 "Baseline MG94xREV":{
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diff changeset
286 "attribute type":"branch length",
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diff changeset
287 "display order":1
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diff changeset
288 },
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iuc
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diff changeset
289 "Baseline MG94xREV omega ratio":{
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iuc
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diff changeset
290 "attribute type":"branch label",
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diff changeset
291 "display order":1
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diff changeset
292 },
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iuc
parents:
diff changeset
293 "Corrected P-value":{
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iuc
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diff changeset
294 "attribute type":"branch label",
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diff changeset
295 "display order":6
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iuc
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diff changeset
296 },
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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diff changeset
297 "Full adaptive model":{
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diff changeset
298 "attribute type":"branch length",
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diff changeset
299 "display order":2
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diff changeset
300 },
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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diff changeset
301 "Full adaptive model (non-synonymous subs/site)":{
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diff changeset
302 "attribute type":"branch label",
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diff changeset
303 "display order":10
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diff changeset
304 },
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diff changeset
305 "Full adaptive model (synonymous subs/site)":{
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diff changeset
306 "attribute type":"branch label",
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diff changeset
307 "display order":9
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diff changeset
308 },
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iuc
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diff changeset
309 "LRT":{
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diff changeset
310 "attribute type":"branch label",
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diff changeset
311 "display order":4
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diff changeset
312 },
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diff changeset
313 "Nucleotide GTR":{
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diff changeset
314 "attribute type":"branch length",
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315 "display order":0
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diff changeset
316 },
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diff changeset
317 "Rate Distributions":{
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diff changeset
318 "attribute type":"branch label",
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319 "display order":3
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diff changeset
320 },
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diff changeset
321 "Rate classes":{
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diff changeset
322 "attribute type":"branch label",
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diff changeset
323 "display order":2
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diff changeset
324 },
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diff changeset
325 "Uncorrected P-value":{
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diff changeset
326 "attribute type":"branch label",
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diff changeset
327 "display order":5
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diff changeset
328 },
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diff changeset
329 "original name":{
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diff changeset
330 "attribute type":"node label",
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diff changeset
331 "display order":-1
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diff changeset
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parents:
diff changeset
333 "rate at which 2 nucleotides are changed instantly within a single codon":{
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diff changeset
334 "attribute type":"branch label",
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diff changeset
335 "display order":7
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parents:
diff changeset
336 }
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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parents:
diff changeset
337 }
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
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diff changeset
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diff changeset
339 "data partitions":{
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diff changeset
340 "0":{
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diff changeset
341 "coverage": [
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diff changeset
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diff changeset
343 ],
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diff changeset
344 "name":"absrel.filter.default"
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parents:
diff changeset
345 }
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diff changeset
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diff changeset
347 "fits":{
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parents:
diff changeset
348 "Baseline MG94xREV":{
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diff changeset
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diff changeset
350 "Equilibrium frequencies": [
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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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iuc
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iuc
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iuc
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iuc
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diff changeset
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iuc
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iuc
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iuc
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iuc
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iuc
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iuc
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iuc
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iuc
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iuc
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iuc
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iuc
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iuc
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iuc
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iuc
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diff changeset
411 [0.01189287130232129]
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iuc
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diff changeset
412 ],
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iuc
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diff changeset
413 "Log Likelihood":-3399.656647852504,
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iuc
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diff changeset
414 "Rate Distributions":{
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iuc
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diff changeset
415 "Per-branch delta":{
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iuc
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diff changeset
416 "2.5%":0,
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iuc
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diff changeset
417 "97.5%":10.66318587577853,
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iuc
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diff changeset
418 "Mean":1.142287895998736,
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iuc
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diff changeset
419 "Median":0.2080459069952131
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diff changeset
420 },
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iuc
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diff changeset
421 "Per-branch omega":{
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iuc
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diff changeset
422 "2.5%":0,
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iuc
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diff changeset
423 "97.5%":2.028136557891868,
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iuc
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diff changeset
424 "Mean":666666667.5178814,
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iuc
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diff changeset
425 "Median":1
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iuc
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diff changeset
426 },
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iuc
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diff changeset
427 "Synonymous site-to-site rates":{
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iuc
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diff changeset
428 "0":{
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iuc
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diff changeset
429 "proportion":0.3499070593950995,
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iuc
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430 "rate":0.3584907731592092
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iuc
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diff changeset
431 },
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iuc
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diff changeset
432 "1":{
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iuc
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diff changeset
433 "proportion":0.5579704535685105,
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iuc
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diff changeset
434 "rate":1.083607309819905
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iuc
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435 },
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iuc
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diff changeset
436 "2":{
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iuc
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diff changeset
437 "proportion":0.09212248703639001,
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iuc
parents:
diff changeset
438 "rate":2.93023662601063
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iuc
parents:
diff changeset
439 }
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iuc
parents:
diff changeset
440 }
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
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diff changeset
441 },
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iuc
parents:
diff changeset
442 "display order":1,
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iuc
parents:
diff changeset
443 "estimated parameters":67
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iuc
parents:
diff changeset
444 },
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iuc
parents:
diff changeset
445 "Full adaptive model":{
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iuc
parents:
diff changeset
446 "AIC-c":6937.867430345418,
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iuc
parents:
diff changeset
447 "Log Likelihood":-3399.405413285916,
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iuc
parents:
diff changeset
448 "Rate Distributions":{
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iuc
parents:
diff changeset
449 },
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iuc
parents:
diff changeset
450 "display order":2,
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iuc
parents:
diff changeset
451 "estimated parameters":67
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iuc
parents:
diff changeset
452 },
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iuc
parents:
diff changeset
453 "Nucleotide GTR":{
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iuc
parents:
diff changeset
454 "AIC-c":7112.857288723968,
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iuc
parents:
diff changeset
455 "Equilibrium frequencies": [
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iuc
parents:
diff changeset
456 [0.3592490842490842],
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iuc
parents:
diff changeset
457 [0.181959706959707],
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iuc
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diff changeset
458 [0.240018315018315],
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iuc
parents:
diff changeset
459 [0.2187728937728937]
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parents:
diff changeset
460 ],
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iuc
parents:
diff changeset
461 "Log Likelihood":-3532.321213744258,
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iuc
parents:
diff changeset
462 "Rate Distributions":{
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iuc
parents:
diff changeset
463 "Substitution rate from nucleotide A to nucleotide C":0.5501644800943087,
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iuc
parents:
diff changeset
464 "Substitution rate from nucleotide A to nucleotide G":1,
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iuc
parents:
diff changeset
465 "Substitution rate from nucleotide A to nucleotide T":0.2646800222727828,
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iuc
parents:
diff changeset
466 "Substitution rate from nucleotide C to nucleotide G":0.4918071762416347,
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iuc
parents:
diff changeset
467 "Substitution rate from nucleotide C to nucleotide T":1.028675134787727,
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iuc
parents:
diff changeset
468 "Substitution rate from nucleotide G to nucleotide T":0.3045013055839741
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iuc
parents:
diff changeset
469 },
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iuc
parents:
diff changeset
470 "display order":0,
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iuc
parents:
diff changeset
471 "estimated parameters":24
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iuc
parents:
diff changeset
472 }
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iuc
parents:
diff changeset
473 },
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iuc
parents:
diff changeset
474 "input":{
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iuc
parents:
diff changeset
475 "file name":"/tmp/tmpasswxnks/job_working_directory/000/9/working/./input.fasta",
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
476 "number of sequences":10,
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
477 "number of sites":187,
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
478 "partition count":1,
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
479 "trees":{
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
480 "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)"
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
481 }
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
482 },
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
483 "runtime":"2.5.36",
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
484 "test results":{
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
485 "P-value threshold":0.05,
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
486 "positive test results":0,
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
487 "tested":16
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
488 },
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
489 "tested":{
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
490 "0":{
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
491 "Baboon":"test",
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
492 "Cat":"test",
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
493 "Chimp":"test",
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
494 "Cow":"test",
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
495 "Horse":"test",
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
496 "Human":"test",
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
497 "Mouse":"test",
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
498 "Node1":"test",
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
499 "Node12":"test",
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
500 "Node2":"test",
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
501 "Node3":"test",
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
502 "Node8":"test",
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
503 "Node9":"test",
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
504 "Pig":"test",
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
505 "Rat":"test",
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
506 "RhMonkey":"test"
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
507 }
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
508 },
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
509 "timers":{
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
510 "Baseline model fitting":{
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
511 "order":2,
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
512 "timer":129
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
513 },
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
514 "Complexity analysis":{
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
515 "order":3,
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
516 "timer":406
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
517 },
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
518 "Full adaptive model fitting":{
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
519 "order":4,
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
520 "timer":46
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
521 },
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
522 "Overall":{
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
523 "order":0,
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
524 "timer":1006
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
525 },
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
526 "Preliminary model fitting":{
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
527 "order":1,
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
528 "timer":0
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
529 },
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
530 "Testing for selection":{
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
531 "order":5,
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
532 "timer":424
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
533 }
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
534 }
49885a825dc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents:
diff changeset
535 }