Mercurial > repos > iuc > hyphy_bgm

annotate test-data/relax-out1.json @ 19:cebcce34d63b 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 22226cfa6cd1eaf04b0a77f4b3a0a9d38430df00"
author iuc
date Thu, 07 Jan 2021 23:20:44 +0000
parents bf97cacc1a55
children d88bbb287923
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bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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1 {
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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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":"RELAX (a random effects test of selection relaxation) uses a random effects branch-site model framework to test whether a set of 'Test' branches evolves under relaxed selection relative to a set of 'Reference' branches (R), as measured by the relaxation parameter (K).\n Version 2.1 adds a check for stability in K estimates to try to mitigate convergence problems",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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4 "version":"2.1",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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5 "citation":"RELAX: Detecting Relaxed Selection in a Phylogenetic Framework (2015). Mol Biol Evol 32 (3): 820-832",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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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"
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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"
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8 "requirements":"in-frame codon alignment and a phylogenetic tree, with at least two groups of branches defined using the {} notation (one group can be defined as all unlabeled branches)"
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"
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10 "input":{
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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11 "file name":"/home/galaxystaging/galaxy/database/jobs_directory/000/79/working/relax_input.fa",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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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"
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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"
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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"
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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"
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18 },
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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19 "fits":{
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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20 "Nucleotide GTR":{
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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21 "Log Likelihood":-3531.964032193222,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
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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":7112.142925621896,
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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":0.5465757107930838,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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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"
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33 "Substitution rate from nucleotide A to nucleotide T":0.264131123736109,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
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34 "Substitution rate from nucleotide C to nucleotide G":0.4861812992450388,
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":1.017887589835735,
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":0.3021773696987065
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"
iuc
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38 "display order":0
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39 },
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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40 "MG94xREV with separate rates for branch sets":{
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41 "Log Likelihood":-3460.931903299487,
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42 "estimated parameters":32,
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43 "AIC-c":6987.013507197776,
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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 "non-synonymous/synonymous rate ratio for *Reference*":[
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diff changeset
109 [1.617765969026557, 1]
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diff changeset
110 ],
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iuc
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diff changeset
111 "non-synonymous/synonymous rate ratio for *Test*":[
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diff changeset
112 [0.7687683974183303, 1]
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diff changeset
113 ]
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diff changeset
114 },
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diff changeset
115 "display order":1
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diff changeset
116 },
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diff changeset
117 "General descriptive":{
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diff changeset
118 "Log Likelihood":-3420.975369746331,
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parents:
diff changeset
119 "estimated parameters":51,
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diff changeset
120 "AIC-c":6946.868231241836,
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iuc
parents:
diff changeset
121 "Rate Distributions":{
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diff changeset
122 "Shared":{
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parents:
diff changeset
123 "0":{
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iuc
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diff changeset
124 "omega":1e-08,
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iuc
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diff changeset
125 "proportion":0.2345034364701236
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iuc
parents:
diff changeset
126 },
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iuc
parents:
diff changeset
127 "1":{
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iuc
parents:
diff changeset
128 "omega":1e-08,
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iuc
parents:
diff changeset
129 "proportion":0.3180344596999608
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iuc
parents:
diff changeset
130 },
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iuc
parents:
diff changeset
131 "2":{
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iuc
parents:
diff changeset
132 "omega":6.64943557055033,
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iuc
parents:
diff changeset
133 "proportion":0.4474621038299156
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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 }
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
136 },
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iuc
parents:
diff changeset
137 "display order":4
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iuc
parents:
diff changeset
138 },
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iuc
parents:
diff changeset
139 "RELAX alternative":{
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iuc
parents:
diff changeset
140 "Log Likelihood":-3429.125323833579,
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iuc
parents:
diff changeset
141 "estimated parameters":36,
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iuc
parents:
diff changeset
142 "AIC-c":6931.704002822642,
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iuc
parents:
diff changeset
143 "Rate Distributions":{
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iuc
parents:
diff changeset
144 "Test":{
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iuc
parents:
diff changeset
145 "0":{
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iuc
parents:
diff changeset
146 "omega":0,
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iuc
parents:
diff changeset
147 "proportion":0.1993913071931658
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iuc
parents:
diff changeset
148 },
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iuc
parents:
diff changeset
149 "1":{
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iuc
parents:
diff changeset
150 "omega":0,
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iuc
parents:
diff changeset
151 "proportion":0.3360341729181165
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iuc
parents:
diff changeset
152 },
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iuc
parents:
diff changeset
153 "2":{
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iuc
parents:
diff changeset
154 "omega":2.153056268947235,
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iuc
parents:
diff changeset
155 "proportion":0.4645745198887177
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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 },
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
158 "Reference":{
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iuc
parents:
diff changeset
159 "0":{
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iuc
parents:
diff changeset
160 "omega":0,
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iuc
parents:
diff changeset
161 "proportion":0.1993913071931658
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iuc
parents:
diff changeset
162 },
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
163 "1":{
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iuc
parents:
diff changeset
164 "omega":0,
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iuc
parents:
diff changeset
165 "proportion":0.3360341729181165
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iuc
parents:
diff changeset
166 },
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
167 "2":{
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iuc
parents:
diff changeset
168 "omega":6.166712663934246,
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iuc
parents:
diff changeset
169 "proportion":0.4645745198887177
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iuc
parents:
diff changeset
170 }
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
171 }
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
172 },
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
173 "display order":2
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diff changeset
174 },
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diff changeset
175 "RELAX null":{
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diff changeset
176 "Log Likelihood":-3437.187429488768,
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diff changeset
177 "estimated parameters":35,
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diff changeset
178 "AIC-c":6945.748904779063,
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diff changeset
179 "Rate Distributions":{
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diff changeset
180 "Test":{
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diff changeset
181 "0":{
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diff changeset
182 "omega":0.1177689533662908,
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diff changeset
183 "proportion":0.4926494715348529
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diff changeset
184 },
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diff changeset
185 "1":{
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diff changeset
186 "omega":0.3195682613972807,
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diff changeset
187 "proportion":0.1517366025099117
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diff changeset
188 },
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diff changeset
189 "2":{
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diff changeset
190 "omega":3.893733071412322,
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diff changeset
191 "proportion":0.3556139259552353
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diff changeset
192 }
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diff changeset
193 },
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diff changeset
194 "Reference":{
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diff changeset
195 "0":{
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diff changeset
196 "omega":0.1177689533662908,
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diff changeset
197 "proportion":0.4926494715348529
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diff changeset
198 },
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diff changeset
199 "1":{
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diff changeset
200 "omega":0.3195682613972807,
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iuc
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diff changeset
201 "proportion":0.1517366025099117
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iuc
parents:
diff changeset
202 },
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iuc
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diff changeset
203 "2":{
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diff changeset
204 "omega":3.893733071412322,
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iuc
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diff changeset
205 "proportion":0.3556139259552353
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iuc
parents:
diff changeset
206 }
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iuc
parents:
diff changeset
207 }
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iuc
parents:
diff changeset
208 },
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iuc
parents:
diff changeset
209 "display order":3
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iuc
parents:
diff changeset
210 },
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iuc
parents:
diff changeset
211 "RELAX partitioned descriptive":{
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iuc
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diff changeset
212 "Log Likelihood":-3427.515821600644,
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iuc
parents:
diff changeset
213 "estimated parameters":40,
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iuc
parents:
diff changeset
214 "AIC-c":6936.824972889643,
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iuc
parents:
diff changeset
215 "Rate Distributions":{
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iuc
parents:
diff changeset
216 "Test":{
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iuc
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diff changeset
217 "0":{
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iuc
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diff changeset
218 "omega":0.2264899618249929,
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iuc
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diff changeset
219 "proportion":0.1370778077745601
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iuc
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diff changeset
220 },
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iuc
parents:
diff changeset
221 "1":{
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iuc
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diff changeset
222 "omega":0.2328054750512875,
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iuc
parents:
diff changeset
223 "proportion":0.6322930022247097
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iuc
parents:
diff changeset
224 },
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iuc
parents:
diff changeset
225 "2":{
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iuc
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diff changeset
226 "omega":4.13407071706127,
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iuc
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diff changeset
227 "proportion":0.2306291900007301
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iuc
parents:
diff changeset
228 }
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iuc
parents:
diff changeset
229 },
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iuc
parents:
diff changeset
230 "Reference":{
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iuc
parents:
diff changeset
231 "0":{
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iuc
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diff changeset
232 "omega":0,
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iuc
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diff changeset
233 "proportion":0.09054841512283768
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iuc
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diff changeset
234 },
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iuc
parents:
diff changeset
235 "1":{
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iuc
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diff changeset
236 "omega":0,
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iuc
parents:
diff changeset
237 "proportion":0.4231976237742962
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iuc
parents:
diff changeset
238 },
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iuc
parents:
diff changeset
239 "2":{
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iuc
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diff changeset
240 "omega":5.975493863572218,
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iuc
parents:
diff changeset
241 "proportion":0.4862539611028661
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iuc
parents:
diff changeset
242 }
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
243 }
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
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diff changeset
244 },
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iuc
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diff changeset
245 "display order":5
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iuc
parents:
diff changeset
246 }
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
247 },
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iuc
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diff changeset
248 "timers":{
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iuc
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diff changeset
249 "Overall":{
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iuc
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diff changeset
250 "timer":562,
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iuc
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diff changeset
251 "order":0
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iuc
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diff changeset
252 },
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iuc
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diff changeset
253 "Preliminary model fitting":{
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diff changeset
254 "timer":33,
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iuc
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diff changeset
255 "order":1
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diff changeset
256 },
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iuc
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diff changeset
257 "General descriptive model fitting":{
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iuc
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diff changeset
258 "timer":256,
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iuc
parents:
diff changeset
259 "order":2
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iuc
parents:
diff changeset
260 },
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iuc
parents:
diff changeset
261 "RELAX alternative model fitting":{
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iuc
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diff changeset
262 "timer":78,
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iuc
parents:
diff changeset
263 "order":3
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iuc
parents:
diff changeset
264 },
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iuc
parents:
diff changeset
265 "RELAX null model fitting":{
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iuc
parents:
diff changeset
266 "timer":98,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
267 "order":4
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
268 },
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
269 "RELAX partitioned descriptive":{
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iuc
parents:
diff changeset
270 "timer":95,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
271 "order":5
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
272 }
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
273 },
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
274 "test results":{
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
275 "LRT":16.12421131037809,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
276 "p-value":5.932080525117289e-05,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
277 "relaxation or intensification parameter":0.4215604262166031
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
278 },
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
279 "tested":{
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
280 "0":{
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
281 "Pig":"Test",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
282 "Cow":"Reference",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
283 "Node3":"Test",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
284 "Horse":"Reference",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
285 "Cat":"Reference",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
286 "Node2":"Test",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
287 "RhMonkey":"Test",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
288 "Baboon":"Test",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
289 "Node9":"Test",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
290 "Human":"Test",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
291 "Chimp":"Test",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
292 "Node12":"Test",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
293 "Node8":"Test",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
294 "Node1":"Test",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
295 "Rat":"Test",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
296 "Mouse":"Test"
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
297 }
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
298 },
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
299 "data partitions":{
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
300 "0":{
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
301 "name":"relax.filter.default",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
302 "coverage":[
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
303 [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]
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
304 ]
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
305 }
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
306 },
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
307 "branch attributes":{
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iuc
parents:
diff changeset
308 "0":{
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iuc
parents:
diff changeset
309 "Human":{
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
310 "original name":"Human",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
311 "Nucleotide GTR":0,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
312 "MG94xREV with separate rates for branch sets":0,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
313 "General descriptive":0,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
314 "k (general descriptive)":0.7168352052656061,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
315 "RELAX alternative":0,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
316 "RELAX null":0,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
317 "RELAX partitioned descriptive":0
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
318 },
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
319 "Chimp":{
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
320 "original name":"Chimp",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
321 "Nucleotide GTR":0.001818722292071369,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
322 "MG94xREV with separate rates for branch sets":0.001828056639868651,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
323 "General descriptive":0.001850581335499795,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
324 "k (general descriptive)":2.329184252362038,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
325 "RELAX alternative":0.001831548027528597,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
326 "RELAX null":0.001835680183060623,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
327 "RELAX partitioned descriptive":0.00183255534978807
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
328 },
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
329 "Baboon":{
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
330 "original name":"Baboon",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
331 "Nucleotide GTR":0.001682319705247233,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
332 "MG94xREV with separate rates for branch sets":0.001770013551346919,
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iuc
parents:
diff changeset
333 "General descriptive":0.001869883333754939,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
334 "k (general descriptive)":0.1228116964827354,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
335 "RELAX alternative":0.001867314836287998,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
336 "RELAX null":0.001853697678697539,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
337 "RELAX partitioned descriptive":0.00189422569191071
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
338 },
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
339 "RhMonkey":{
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
340 "original name":"RhMonkey",
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
341 "Nucleotide GTR":0.003776495523121213,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
342 "MG94xREV with separate rates for branch sets":0.003720554271464007,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
343 "General descriptive":0.003663070393385353,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
344 "k (general descriptive)":2.272939790126477,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
345 "RELAX alternative":0.003641537789305734,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
346 "RELAX null":0.003670955010908306,
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
347 "RELAX partitioned descriptive":0.003632158699516803
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
348 },
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
349 "Cow":{
bf97cacc1a55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
350 "original name":"Cow",
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iuc
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diff changeset
351 "Nucleotide GTR":0.2483201583381086,
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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
354 "k (general descriptive)":1.19957642031092,
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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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iuc
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diff changeset
358 },
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iuc
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diff changeset
359 "Pig":{
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iuc
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diff changeset
360 "original name":"Pig",
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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
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iuc
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iuc
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iuc
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diff changeset
368 },
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iuc
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diff changeset
369 "Horse":{
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iuc
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diff changeset
370 "original name":"Horse",
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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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iuc
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iuc
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diff changeset
378 },
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iuc
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diff changeset
379 "Cat":{
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iuc
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diff changeset
380 "original name":"Cat",
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iuc
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diff changeset
381 "Nucleotide GTR":0.2660040109418023,
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
388 },
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iuc
parents:
diff changeset
389 "Mouse":{
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iuc
parents:
diff changeset
390 "original name":"Mouse",
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iuc
parents:
diff changeset
391 "Nucleotide GTR":0.1182531454610134,
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
parents:
diff changeset
398 },
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iuc
parents:
diff changeset
399 "Rat":{
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iuc
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diff changeset
400 "original name":"Rat",
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iuc
parents:
diff changeset
401 "Nucleotide GTR":0.06669544716210057,
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diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
parents:
diff changeset
408 },
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iuc
parents:
diff changeset
409 "Node1":{
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iuc
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diff changeset
410 "Nucleotide GTR":0.2771601504028877,
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diff changeset
412 "General descriptive":0.3532216661512288,
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iuc
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diff changeset
413 "k (general descriptive)":0.2199586786715634,
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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
416 "RELAX partitioned descriptive":0.4360897576025625
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iuc
parents:
diff changeset
417 },
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iuc
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diff changeset
418 "Node12":{
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diff changeset
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diff changeset
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diff changeset
421 "General descriptive":0.01771170858901891,
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diff changeset
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diff changeset
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diff changeset
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diff changeset
425 "RELAX partitioned descriptive":0.01877701767421286
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diff changeset
426 },
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diff changeset
427 "Node2":{
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iuc
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diff changeset
428 "Nucleotide GTR":0.06619118337434968,
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diff changeset
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diff changeset
430 "General descriptive":0.05843310574046084,
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iuc
parents:
diff changeset
431 "k (general descriptive)":0.2816499194095207,
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iuc
parents:
diff changeset
432 "RELAX alternative":0.05469841675490748,
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iuc
parents:
diff changeset
433 "RELAX null":0.06219694236954142,
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iuc
parents:
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463 },
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469 "Nucleotide GTR":{
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484 },
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485 "RELAX alternative":{
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487 "display order":2
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488 },
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489 "RELAX null":{
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diff changeset
490 "attribute type":"branch length",
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diff changeset
491 "display order":3
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492 },
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493 "RELAX partitioned descriptive":{
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diff changeset
494 "attribute type":"branch length",
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diff changeset
495 "display order":5
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diff changeset
496 }
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iuc
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diff changeset
497 }
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iuc
parents:
diff changeset
498 }
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parents:
diff changeset
499 }