Mercurial > repos > iuc > hyphy_bgm

annotate test-data/absrel-out1.json @ 9:0669558ebc6b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8abccd4b7a288b6a321a6662eec88577ad83b36f"
author iuc
date Wed, 22 Apr 2020 12:13:15 -0400
parents bf97cacc1a55
children 91006eb8b84e
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
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1 {
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
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2 "analysis":{
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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3 "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.",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
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4 "version":"2.0",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
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5 "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",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
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6 "authors":"Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution group",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
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7 "contact":"spond@temple.edu",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
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8 "requirements":"in-frame codon alignment and a phylogenetic tree"
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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9 },
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
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10 "input":{
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
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11 "file name":"/tmp/tmpCAMqUO/job_working_directory/002/2602/working/absrel_input.fa",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
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12 "number of sequences":10,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
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13 "number of sites":187,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
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14 "partition count":1,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
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15 "trees":{
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
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16 "0":"((((Pig:0.147969,Cow:0.21343)Node3:0.085099,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)"
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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17 }
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
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18 },
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
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19 "fits":{
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
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20 "Nucleotide GTR":{
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
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21 "Log Likelihood":-3531.96369518556,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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22 "estimated parameters":24,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
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23 "AIC-c":7112.577796875186,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
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24 "Equilibrium frequencies":[
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29 ],
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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30 "Rate Distributions":{
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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31 "Substitution rate from nucleotide A to nucleotide C":0.5474707834424497,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
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32 "Substitution rate from nucleotide A to nucleotide G":1,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
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33 "Substitution rate from nucleotide A to nucleotide T":0.2645731370379643,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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34 "Substitution rate from nucleotide C to nucleotide G":0.4867482826410435,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
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35 "Substitution rate from nucleotide C to nucleotide T":1.018295973581558,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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36 "Substitution rate from nucleotide G to nucleotide T":0.3026112531229544
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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37 },
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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38 "display order":0
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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39 },
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40 "Baseline MG94xREV":{
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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41 "Log Likelihood":-3450.669934819203,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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42 "estimated parameters":46,
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43 "AIC-c":6995.711784065174,
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44 "Equilibrium frequencies":[
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diff changeset
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diff changeset
106 ],
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diff changeset
107 "Rate Distributions":{
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diff changeset
108 "Per-branch omega":{
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diff changeset
109 "Mean":666666667.6064719,
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diff changeset
110 "Median":1.103169534345197,
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diff changeset
111 "2.5%":0,
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diff changeset
112 "97.5%":10000000000
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diff changeset
113 }
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diff changeset
114 },
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iuc
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diff changeset
115 "display order":1
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diff changeset
116 },
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diff changeset
117 "Full adaptive model":{
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diff changeset
118 "Log Likelihood":-3414.992415597899,
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diff changeset
119 "estimated parameters":60,
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iuc
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diff changeset
120 "AIC-c":6954.031265689993,
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iuc
parents:
diff changeset
121 "Rate Distributions":{
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iuc
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diff changeset
122 },
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
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diff changeset
123 "display order":2
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iuc
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diff changeset
124 }
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iuc
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diff changeset
125 },
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
126 "timers":{
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iuc
parents:
diff changeset
127 "Overall":{
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iuc
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diff changeset
128 "timer":98,
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iuc
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diff changeset
129 "order":0
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iuc
parents:
diff changeset
130 },
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
131 "Preliminary model fitting":{
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iuc
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diff changeset
132 "timer":0,
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iuc
parents:
diff changeset
133 "order":1
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
134 },
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
135 "Baseline model fitting":{
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iuc
parents:
diff changeset
136 "timer":1,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
137 "order":2
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
138 },
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
139 "Complexity analysis":{
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
140 "timer":36,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
141 "order":3
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
142 },
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
143 "Full adaptive model fitting":{
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
144 "timer":8,
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iuc
parents:
diff changeset
145 "order":4
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iuc
parents:
diff changeset
146 },
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
147 "Testing for selection":{
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
148 "timer":53,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
149 "order":5
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
150 }
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
151 },
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
152 "test results":{
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
153 "P-value threshold":0.05,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
154 "tested":16,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
155 "positive test results":3
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
156 },
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
157 "tested":{
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
158 "0":{
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
159 "Pig":"test",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
160 "Cow":"test",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
161 "Node3":"test",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
162 "Horse":"test",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
163 "Cat":"test",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
164 "Node2":"test",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
165 "RhMonkey":"test",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
166 "Baboon":"test",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
167 "Node9":"test",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
168 "Human":"test",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
169 "Chimp":"test",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
170 "Node12":"test",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
171 "Node8":"test",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
172 "Node1":"test",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
173 "Rat":"test",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
174 "Mouse":"test"
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iuc
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diff changeset
175 }
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iuc
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diff changeset
176 },
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diff changeset
177 "data partitions":{
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diff changeset
178 "0":{
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diff changeset
179 "name":"absrel.filter.default",
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diff changeset
180 "coverage":[
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iuc
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diff changeset
181 [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]
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iuc
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diff changeset
182 ]
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diff changeset
183 }
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iuc
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diff changeset
184 },
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iuc
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diff changeset
185 "branch attributes":{
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diff changeset
186 "0":{
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diff changeset
187 "Human":{
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diff changeset
188 "original name":"Human",
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diff changeset
189 "Nucleotide GTR":0,
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iuc
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diff changeset
190 "Baseline MG94xREV":0,
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iuc
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diff changeset
191 "Baseline MG94xREV omega ratio":1,
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iuc
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diff changeset
192 "Rate classes":1,
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iuc
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diff changeset
193 "Full adaptive model":0,
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iuc
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diff changeset
194 "Rate Distributions":[
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iuc
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diff changeset
195 [1, 1]
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diff changeset
196 ],
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diff changeset
197 "LRT":0,
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diff changeset
198 "Uncorrected P-value":1,
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iuc
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diff changeset
199 "Corrected P-value":1
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iuc
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diff changeset
200 },
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iuc
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diff changeset
201 "Chimp":{
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iuc
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diff changeset
202 "original name":"Chimp",
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iuc
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diff changeset
203 "Nucleotide GTR":0.001818174796225333,
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diff changeset
204 "Baseline MG94xREV":0.001839770270131542,
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iuc
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diff changeset
205 "Baseline MG94xREV omega ratio":10000000000,
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iuc
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diff changeset
206 "Rate classes":1,
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iuc
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diff changeset
207 "Full adaptive model":0.001845806111200226,
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iuc
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diff changeset
208 "Rate Distributions":[
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iuc
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diff changeset
209 [10000000000, 1]
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iuc
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diff changeset
210 ],
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iuc
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diff changeset
211 "LRT":0.6362875427803374,
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iuc
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diff changeset
212 "Uncorrected P-value":0.303261123771571,
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iuc
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diff changeset
213 "Corrected P-value":1
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iuc
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diff changeset
214 },
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iuc
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diff changeset
215 "Baboon":{
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iuc
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diff changeset
216 "original name":"Baboon",
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iuc
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diff changeset
217 "Nucleotide GTR":0.001682034724848474,
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iuc
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diff changeset
218 "Baseline MG94xREV":0.001821072110941238,
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iuc
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diff changeset
219 "Baseline MG94xREV omega ratio":0,
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iuc
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diff changeset
220 "Rate classes":1,
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iuc
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diff changeset
221 "Full adaptive model":0.001808294153407354,
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iuc
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diff changeset
222 "Rate Distributions":[
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iuc
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diff changeset
223 [0, 1]
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iuc
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diff changeset
224 ],
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iuc
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diff changeset
225 "LRT":0,
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iuc
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diff changeset
226 "Uncorrected P-value":1,
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iuc
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diff changeset
227 "Corrected P-value":1
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iuc
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diff changeset
228 },
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iuc
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diff changeset
229 "RhMonkey":{
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iuc
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diff changeset
230 "original name":"RhMonkey",
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iuc
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diff changeset
231 "Nucleotide GTR":0.003775509884015639,
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iuc
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diff changeset
232 "Baseline MG94xREV":0.003671340584166445,
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iuc
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diff changeset
233 "Baseline MG94xREV omega ratio":10000000000,
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iuc
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diff changeset
234 "Rate classes":1,
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iuc
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diff changeset
235 "Full adaptive model":0.003682180830540259,
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iuc
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diff changeset
236 "Rate Distributions":[
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iuc
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diff changeset
237 [10000000000, 1]
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iuc
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diff changeset
238 ],
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iuc
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diff changeset
239 "LRT":1.200615147074132,
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iuc
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diff changeset
240 "Uncorrected P-value":0.2192326116145807,
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iuc
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diff changeset
241 "Corrected P-value":1
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iuc
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diff changeset
242 },
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iuc
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diff changeset
243 "Cow":{
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iuc
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diff changeset
244 "original name":"Cow",
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iuc
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diff changeset
245 "Nucleotide GTR":0.248257545271419,
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iuc
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diff changeset
246 "Baseline MG94xREV":0.2535517510207829,
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iuc
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diff changeset
247 "Baseline MG94xREV omega ratio":1.957039676836281,
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iuc
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diff changeset
248 "Rate classes":2,
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iuc
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diff changeset
249 "Full adaptive model":0.3959632497370367,
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iuc
parents:
diff changeset
250 "Rate Distributions":[
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diff changeset
251 [0, 0.5384412409742189],
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iuc
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diff changeset
252 [10.58123012791267, 0.4615587590257811]
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diff changeset
253 ],
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iuc
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diff changeset
254 "LRT":24.50128746473001,
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iuc
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diff changeset
255 "Uncorrected P-value":1.583131814197891e-06,
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iuc
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diff changeset
256 "Corrected P-value":2.533010902716626e-05
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iuc
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diff changeset
257 },
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iuc
parents:
diff changeset
258 "Pig":{
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iuc
parents:
diff changeset
259 "original name":"Pig",
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diff changeset
260 "Nucleotide GTR":0.1872143003439852,
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diff changeset
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iuc
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diff changeset
262 "Baseline MG94xREV omega ratio":1.354835319497051,
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diff changeset
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iuc
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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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diff changeset
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diff changeset
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diff changeset
272 "Horse":{
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diff changeset
273 "original name":"Horse",
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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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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
287 "Cat":{
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diff changeset
288 "original name":"Cat",
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diff changeset
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iuc
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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
294 "Rate Distributions":[
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iuc
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diff changeset
296 [6.025097508634321, 0.4224987258994394]
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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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diff changeset
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iuc
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diff changeset
302 "Mouse":{
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diff changeset
303 "original name":"Mouse",
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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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diff changeset
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diff changeset
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diff changeset
309 "Rate Distributions":[
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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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diff changeset
315 },
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iuc
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diff changeset
316 "Rat":{
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iuc
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diff changeset
317 "original name":"Rat",
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iuc
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diff changeset
318 "Nucleotide GTR":0.06673994656462794,
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diff changeset
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iuc
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diff changeset
320 "Baseline MG94xREV omega ratio":1.103169534345197,
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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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diff changeset
329 },
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iuc
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diff changeset
330 "Node1":{
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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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diff changeset
336 "Rate Distributions":[
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diff changeset
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diff changeset
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339 ],
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diff changeset
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diff changeset
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diff changeset
342 "Corrected P-value":1
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diff changeset
343 },
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iuc
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diff changeset
344 "Node12":{
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diff changeset
345 "Nucleotide GTR":0.01783922546179193,
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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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diff changeset
385 "Node8":{
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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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diff changeset
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diff changeset
399 "Node9":{
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diff changeset
400 "Nucleotide GTR":0.02566719422260768,
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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
405 "Rate Distributions":[
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diff changeset
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410 "Corrected P-value":1
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diff changeset
411 }
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412 },
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413 "attributes":{
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414 "original name":{
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415 "attribute type":"node label",
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416 "display order":-1
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417 },
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diff changeset
418 "Nucleotide GTR":{
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420 "display order":0
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422 "Baseline MG94xREV":{
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423 "attribute type":"branch length",
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424 "display order":1
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425 },
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diff changeset
426 "Baseline MG94xREV omega ratio":{
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427 "attribute type":"branch label",
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diff changeset
428 "display order":1
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429 },
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diff changeset
430 "Rate classes":{
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diff changeset
431 "attribute type":"branch label",
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diff changeset
432 "display order":2
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diff changeset
433 },
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diff changeset
434 "Full adaptive model":{
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
435 "attribute type":"branch length",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
436 "display order":2
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
437 },
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
438 "Rate Distributions":{
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
439 "attribute type":"branch label",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
440 "display order":3
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
441 },
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
442 "LRT":{
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
443 "attribute type":"branch label",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
444 "display order":4
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
445 },
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
446 "Uncorrected P-value":{
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
447 "attribute type":"branch label",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
448 "display order":5
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
449 },
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
450 "Corrected P-value":{
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
451 "attribute type":"branch label",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
452 "display order":6
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
453 }
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
454 }
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
455 }
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
456 }