Mercurial > repos > iuc > hyphy_fade

annotate test-data/busted-out1.json @ 29:fccaa7ba05fd draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ec5db8349483b2cd46f9da23abe6cefcf65bc714"
author iuc
date Sat, 03 Jul 2021 08:54:30 +0000
parents 5e8d0e777033
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
1 {
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da4192d32e10 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
iuc
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diff changeset
2 "Evidence Ratios":{
da4192d32e10 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
iuc
parents: 0
diff changeset
3 "constrained": [
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5e8d0e777033 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
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diff changeset
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da4192d32e10 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
iuc
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diff changeset
5 ],
da4192d32e10 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
iuc
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diff changeset
6 "optimized null": [
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iuc
parents: 1
diff changeset
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da4192d32e10 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
iuc
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diff changeset
8 ]
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6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
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diff changeset
9 },
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da4192d32e10 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
iuc
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diff changeset
10 "Site Log Likelihood":{
da4192d32e10 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
iuc
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diff changeset
11 "constrained": [
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iuc
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diff changeset
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da4192d32e10 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
iuc
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13 ],
da4192d32e10 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
iuc
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diff changeset
14 "optimized null": [
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iuc
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da4192d32e10 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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16 ],
da4192d32e10 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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17 "unconstrained": [
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5e8d0e777033 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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da4192d32e10 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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da4192d32e10 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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20 },
da4192d32e10 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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21 "Synonymous site-posteriors": [
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5e8d0e777033 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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5e8d0e777033 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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5e8d0e777033 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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da4192d32e10 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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25 ],
da4192d32e10 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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diff changeset
26 "analysis":{
da4192d32e10 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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27 "authors":"Sergei L Kosakovsky Pond",
da4192d32e10 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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diff changeset
28 "citation":"*Gene-wide identification of episodic selection*, Mol Biol Evol. 32(5):1365-71",
da4192d32e10 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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diff changeset
29 "contact":"spond@temple.edu",
25
5e8d0e777033 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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diff changeset
30 "info":"BUSTED (branch-site unrestricted statistical test of episodic diversification) uses a random effects branch-site model fitted \njointly to all or a subset of tree branches in order to test for alignment-wide evidence of episodic diversifying selection. \nAssuming there is evidence of positive selection (i.e. there is an omega > 1), BUSTED will also perform a quick evidence-ratio \nstyle analysis to explore which individual sites may have been subject to selection. v2.0 adds support for synonymous rate variation, \nand relaxes the test statistic to 0.5 (chi^2_0 + chi^2_2). Version 2.1 adds a grid search for the initial starting point.\nVersion 2.2 changes the grid search to LHC, and adds an initial search phase to use adaptive Nedler-Mead. Version 3.0 implements the option\nfor branch-site variation in synonymous substitution rates. Version 3.1 adds HMM auto-correlation option for SRV, and binds SRV distributions for multiple branch sets\n",
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da4192d32e10 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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diff changeset
31 "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})",
25
5e8d0e777033 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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diff changeset
32 "version":"3.1"
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6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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diff changeset
33 },
6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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diff changeset
34 "background":0,
6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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35 "branch attributes":{
6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
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36 "0":{
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37 "Baboon":{
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5e8d0e777033 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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38 "MG94xREV with separate rates for branch sets":0.001772434847524003,
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iuc
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39 "Nucleotide GTR":0.001680040630127455,
5e8d0e777033 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
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40 "constrained":0.001513413708231178,
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6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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diff changeset
41 "original name":"Baboon",
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5e8d0e777033 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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42 "unconstrained":0.00161713005248515
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43 },
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44 "Cat":{
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5e8d0e777033 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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45 "MG94xREV with separate rates for branch sets":0.2735065373507703,
5e8d0e777033 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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46 "Nucleotide GTR":0.2660909938917123,
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47 "constrained":0.3466844629529476,
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6164d9298db9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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diff changeset
48 "original name":"Cat",
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5e8d0e777033 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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49 "unconstrained":0.3607268493024173
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da4192d32e10 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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50 },
da4192d32e10 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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diff changeset
51 "Chimp":{
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5e8d0e777033 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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52 "MG94xREV with separate rates for branch sets":0.001828401123834132,
5e8d0e777033 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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53 "Nucleotide GTR":0.001818373670119325,
5e8d0e777033 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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54 "constrained":0.001854421055569225,
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da4192d32e10 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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diff changeset
55 "original name":"Chimp",
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5e8d0e777033 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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56 "unconstrained":0.001853794709397617
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da4192d32e10 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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57 },
da4192d32e10 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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58 "Cow":{
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5e8d0e777033 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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59 "MG94xREV with separate rates for branch sets":0.2477981038577003,
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60 "Nucleotide GTR":0.2481025999892287,
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61 "constrained":0.3115800338446564,
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da4192d32e10 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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62 "original name":"Cow",
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63 "unconstrained":0.3266266518611717
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64 },
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65 "Horse":{
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iuc
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iuc
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iuc
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iuc
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iuc
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iuc
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104 "Node3":{
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110 "Node8":{
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116 "Node9":{
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122 "Pig":{
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126 "original name":"Pig",
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128 },
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129 "Rat":{
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131 "Nucleotide GTR":0.06661283005976348,
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132 "constrained":0.06832918896283274,
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133 "original name":"Rat",
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134 "unconstrained":0.07114161288708017
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135 },
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136 "RhMonkey":{
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138 "Nucleotide GTR":0.003775170135617877,
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139 "constrained":0.004078975866589158,
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iuc
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140 "original name":"RhMonkey",
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142 }
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iuc
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144 "attributes":{
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147 "display order":1
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148 },
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149 "Nucleotide GTR":{
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iuc
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diff changeset
150 "attribute type":"branch length",
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151 "display order":0
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152 },
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153 "constrained":{
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154 "attribute type":"branch length",
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155 "display order":1
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156 },
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157 "original name":{
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158 "attribute type":"node label",
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159 "display order":0
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161 "unconstrained":{
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162 "attribute type":"branch length",
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167 "data partitions":{
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169 "coverage": [
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170 [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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172 "name":"busted.filter.default"
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175 "fits":{
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176 "Constrained model":{
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177 "AIC-c":6918.865252134614,
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178 "Log Likelihood":-3419.580167050914,
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179 "Rate Distributions":{
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180 "Synonymous site-to-site rates":{
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181 "0":{
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182 "proportion":0.3286044813984554,
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183 "rate":0.3114745230555425
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189 "2":{
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190 "proportion":0.09548817003986594,
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194 "Test":{
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199 "1":{
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202 },
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203 "2":{
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204 "omega":1,
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205 "proportion":0.8389662540476177
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207 }
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208 },
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209 "display order":3,
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210 "estimated parameters":39
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211 },
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212 "MG94xREV with separate rates for branch sets":{
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213 "AIC-c":6997.104847699299,
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214 "Equilibrium frequencies": [
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276 ],
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277 "Log Likelihood":-3467.012706765863,
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278 "Rate Distributions":{
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279 "non-synonymous/synonymous rate ratio for *test*": [
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280 [0.9959842858928788, 1]
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281 ]
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282 },
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283 "display order":1,
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284 "estimated parameters":31
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285 },
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286 "Nucleotide GTR":{
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iuc
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287 "AIC-c":7112.857310169033,
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diff changeset
288 "Equilibrium frequencies": [
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292 [0.2187728937728937]
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293 ],
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294 "Log Likelihood":-3532.32122446679,
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295 "Rate Distributions":{
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296 "Substitution rate from nucleotide A to nucleotide C":0.5501644800943087,
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diff changeset
297 "Substitution rate from nucleotide A to nucleotide G":1,
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iuc
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298 "Substitution rate from nucleotide A to nucleotide T":0.2647746107611847,
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diff changeset
299 "Substitution rate from nucleotide C to nucleotide G":0.4917423221832032,
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diff changeset
300 "Substitution rate from nucleotide C to nucleotide T":1.02837595903795,
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diff changeset
301 "Substitution rate from nucleotide G to nucleotide T":0.304509117524575
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302 },
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diff changeset
303 "display order":0,
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iuc
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diff changeset
304 "estimated parameters":24
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305 },
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diff changeset
306 "Unconstrained model":{
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iuc
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307 "AIC-c":6910.776988890891,
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iuc
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diff changeset
308 "Log Likelihood":-3414.491829601268,
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diff changeset
309 "Rate Distributions":{
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iuc
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diff changeset
310 "Synonymous site-to-site rates":{
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iuc
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diff changeset
311 "0":{
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iuc
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diff changeset
312 "proportion":0.2655037162058198,
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iuc
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diff changeset
313 "rate":0.2749303122566129
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diff changeset
314 },
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iuc
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diff changeset
315 "1":{
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iuc
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diff changeset
316 "proportion":0.6321791898264187,
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iuc
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diff changeset
317 "rate":0.9740711294478059
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diff changeset
318 },
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340 "estimated parameters":40
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343 "input":{
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344 "file name":"/tmp/tmpfqvtss8b/job_working_directory/000/3/working/./input.fasta",
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345 "number of sequences":10,
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348 "trees":{
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349 "0":"((((Pig:0.147969,Cow:0.21343)Node3:0.08509899999999999,Horse:0.165787,Cat:0.264806)Node2:0.058611,((RhMonkey:0.002015,Baboon:0.003108)Node9:0.022733,(Human:0.004349,Chimp:0.000799)Node12:0.011873)Node8:0.101856)Node1:0.340802,Rat:0.050958,Mouse:0.09795)"
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352 "test results":{
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353 "LRT":10.17667489929045,
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354 "p-value":0.003084133210483175
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358 "Baboon":"test",
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359 "Cat":"test",
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360 "Chimp":"test",
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361 "Cow":"test",
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362 "Horse":"test",
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363 "Human":"test",
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364 "Mouse":"test",
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365 "Node1":"test",
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366 "Node12":"test",
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367 "Node2":"test",
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368 "Node3":"test",
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369 "Node8":"test",
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370 "Node9":"test",
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371 "Pig":"test",
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372 "Rat":"test",
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373 "RhMonkey":"test"
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376 "timers":{
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377 "Constrained BUSTED model fitting":{
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378 "order":3,
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379 "timer":70
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381 "Overall":{
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385 "Preliminary model fitting":{
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389 "Unconstrained BUSTED model fitting":{
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391 "timer":370
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