Mercurial > repos > iuc > hyphy_cfel

annotate test-data/summary/nsp8.BUSTED.json @ 3:c046f72e5e3a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
author iuc
date Wed, 09 Jun 2021 06:58:21 +0000
parents
children
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3
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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diff changeset
1 {
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
2 "Evidence Ratios":{
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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diff changeset
3 "constrained": [
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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diff changeset
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c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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diff changeset
5 ],
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
6 "optimized null": [
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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diff changeset
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c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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diff changeset
8 ]
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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diff changeset
9 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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diff changeset
10 "Site Log Likelihood":{
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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diff changeset
11 "constrained": [
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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diff changeset
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c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
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13 ],
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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14 "optimized null": [
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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diff changeset
16 ],
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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diff changeset
17 "unconstrained": [
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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diff changeset
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c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
19 ]
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
20 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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diff changeset
21 "Synonymous site-posteriors": [
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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diff changeset
22 [1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1],
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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diff changeset
23 [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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diff changeset
24 [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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diff changeset
25 ],
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
26 "analysis":{
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
27 "authors":"Sergei L Kosakovsky Pond",
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
28 "citation":"*Gene-wide identification of episodic selection*, Mol Biol Evol. 32(5):1365-71",
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
29 "contact":"spond@temple.edu",
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
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",
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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diff changeset
31 "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})",
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
32 "version":"3.1"
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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diff changeset
33 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
34 "background":1,
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
35 "branch attributes":{
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
36 "0":{
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
37 "Node20":{
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
38 "MG94xREV with separate rates for branch sets":0.001634413111521572,
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
39 "Nucleotide GTR":0.001684521619549293,
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
40 "constrained":0.001693211721917988,
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
41 "unconstrained":0.001634737470752693
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
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parents:
diff changeset
42 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
43 "Node38":{
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
44 "MG94xREV with separate rates for branch sets":0.001735516181117074,
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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diff changeset
45 "Nucleotide GTR":0.00168484920326581,
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iuc
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diff changeset
46 "constrained":0.001746636597224389,
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iuc
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diff changeset
47 "unconstrained":0.001745922493640185
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iuc
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diff changeset
48 },
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iuc
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diff changeset
49 "Node4":{
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iuc
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iuc
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52 "constrained":0.00169237478895786,
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iuc
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53 "unconstrained":0.001634679276807916
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iuc
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55 "REFERENCE":{
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iuc
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iuc
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iuc
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iuc
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59 "original name":"REFERENCE",
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iuc
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60 "unconstrained":0
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iuc
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61 },
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iuc
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62 "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":{
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iuc
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64 "Nucleotide GTR":0,
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iuc
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65 "constrained":0,
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iuc
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diff changeset
66 "original name":"epi_isl_1181694/hCoV-19/USA/DE-DHSS-B1064373/2021",
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iuc
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67 "unconstrained":0
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iuc
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iuc
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69 "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":{
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iuc
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71 "Nucleotide GTR":0.001682745450340891,
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iuc
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72 "constrained":0.001740810892619706,
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iuc
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73 "original name":"epi_isl_1357692/hCoV-19/India/WB-1931500870015/2021",
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iuc
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74 "unconstrained":0.001741861798096834
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iuc
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75 },
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iuc
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76 "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":{
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iuc
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78 "Nucleotide GTR":0,
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iuc
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79 "constrained":0,
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iuc
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diff changeset
80 "original name":"epi_isl_1384851/hCoV-19/India/MH-NCCS-ND13683/2021",
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iuc
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81 "unconstrained":0
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iuc
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82 },
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iuc
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83 "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":{
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iuc
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iuc
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85 "Nucleotide GTR":0.00168274558227101,
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iuc
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86 "constrained":0.001724598894711448,
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iuc
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87 "original name":"epi_isl_1415270/hCoV-19/India/MH-NCCS-BJ2/2021",
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iuc
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88 "unconstrained":0.00172378454888454
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iuc
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89 },
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iuc
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90 "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":{
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iuc
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92 "Nucleotide GTR":0.001684401404203384,
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iuc
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93 "constrained":0.001729230796728467,
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iuc
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94 "original name":"epi_isl_1416968/hCoV-19/Guadeloupe/IPP06229/2021",
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iuc
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95 "unconstrained":0.001728407952232285
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iuc
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96 },
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iuc
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97 "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":{
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iuc
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98 "MG94xREV with separate rates for branch sets":0.001732400224912789,
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iuc
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99 "Nucleotide GTR":0.00168406792173386,
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iuc
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100 "constrained":0.001742560499558777,
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iuc
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diff changeset
101 "original name":"epi_isl_1533793/hCoV-19/India/MH-NCCS-CHN21027888/2021",
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iuc
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102 "unconstrained":0.001741714354731224
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iuc
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103 },
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iuc
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diff changeset
104 "epi_isl_1543980_hCoV_19_Singapore_490_2021":{
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iuc
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105 "MG94xREV with separate rates for branch sets":0.001734572372208465,
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iuc
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106 "Nucleotide GTR":0.001684975469042935,
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iuc
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107 "constrained":0.001731729790734787,
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iuc
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108 "original name":"epi_isl_1543980/hCoV-19/Singapore/490/2021",
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iuc
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109 "unconstrained":0.001732786109469241
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iuc
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110 },
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iuc
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diff changeset
111 "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":{
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iuc
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112 "MG94xREV with separate rates for branch sets":0.001735567212787407,
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iuc
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113 "Nucleotide GTR":0.001684401583391051,
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iuc
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114 "constrained":0.001747074976659773,
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iuc
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diff changeset
115 "original name":"epi_isl_1544068/hCoV-19/India/MH-NCCS-RT231527/2021",
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iuc
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116 "unconstrained":0.001746237158517961
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iuc
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117 },
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iuc
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118 "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":{
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iuc
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119 "MG94xREV with separate rates for branch sets":0.001732287290590118,
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iuc
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120 "Nucleotide GTR":0.001682745512695379,
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iuc
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121 "constrained":0.001740808563096063,
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iuc
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diff changeset
122 "original name":"epi_isl_1573247/hCoV-19/Germany/un-RKI-I-068985/2021",
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iuc
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123 "unconstrained":0.001741859812945089
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iuc
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124 },
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iuc
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diff changeset
125 "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":{
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iuc
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126 "MG94xREV with separate rates for branch sets":0,
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iuc
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diff changeset
127 "Nucleotide GTR":0,
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iuc
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diff changeset
128 "constrained":0,
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iuc
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diff changeset
129 "original name":"epi_isl_1589870/hCoV-19/India/WB-1931501009078/2021",
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iuc
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diff changeset
130 "unconstrained":0
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iuc
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diff changeset
131 },
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iuc
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diff changeset
132 "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":{
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iuc
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134 "Nucleotide GTR":0.001684431017860219,
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iuc
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135 "constrained":0.001734525657950819,
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iuc
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diff changeset
136 "original name":"epi_isl_1589885/hCoV-19/India/WB-1931300250528/2021",
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iuc
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137 "unconstrained":0.001733797611044031
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iuc
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138 },
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iuc
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139 "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":{
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iuc
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141 "Nucleotide GTR":0.001684439221071522,
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iuc
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142 "constrained":0.001734525641075956,
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iuc
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diff changeset
143 "original name":"epi_isl_1592421/hCoV-19/USA/MA-CDC-STM-000044850/2021",
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iuc
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144 "unconstrained":0.001733797586870458
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iuc
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145 },
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iuc
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diff changeset
146 "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":{
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iuc
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147 "MG94xREV with separate rates for branch sets":0,
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iuc
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148 "Nucleotide GTR":0,
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iuc
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149 "constrained":0,
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iuc
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diff changeset
150 "original name":"epi_isl_1615709/hCoV-19/England/CAMC-14E792B/2021",
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iuc
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151 "unconstrained":0
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152 },
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iuc
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153 "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":{
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iuc
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155 "Nucleotide GTR":0.00168443927661716,
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iuc
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156 "constrained":0.001747480008189039,
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iuc
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157 "original name":"epi_isl_1632256/hCoV-19/England/RAND-14E1D70/2021",
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iuc
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158 "unconstrained":0.001746773965693989
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iuc
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159 },
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iuc
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160 "epi_isl_1652105_hCoV_19_Singapore_561_2021":{
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iuc
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162 "Nucleotide GTR":0.001685171120971631,
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iuc
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163 "constrained":0.001732690281328906,
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iuc
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164 "original name":"epi_isl_1652105/hCoV-19/Singapore/561/2021",
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iuc
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165 "unconstrained":0.001731872572618556
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iuc
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166 },
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iuc
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167 "epi_isl_1652118_hCoV_19_Singapore_575_2021":{
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168 "MG94xREV with separate rates for branch sets":0.001733317353430654,
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iuc
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169 "Nucleotide GTR":0.001684401899924961,
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iuc
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170 "constrained":0.001730463712944027,
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iuc
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171 "original name":"epi_isl_1652118/hCoV-19/Singapore/575/2021",
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iuc
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172 "unconstrained":0.001729680833222066
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iuc
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173 },
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iuc
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174 "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":{
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175 "MG94xREV with separate rates for branch sets":0.01050948249148799,
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iuc
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176 "Nucleotide GTR":0.01020457779555702,
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iuc
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177 "constrained":0.01044120365653111,
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iuc
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178 "original name":"gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human",
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iuc
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179 "unconstrained":0.01043688886686767
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iuc
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180 },
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iuc
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181 "gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human":{
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182 "MG94xREV with separate rates for branch sets":0.0268366757984672,
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iuc
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183 "Nucleotide GTR":0.02592331511084145,
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iuc
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184 "constrained":0.02709485950713109,
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iuc
parents:
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185 "original name":"gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human",
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iuc
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186 "unconstrained":0.02711261487921226
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iuc
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187 },
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iuc
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diff changeset
188 "gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human":{
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iuc
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189 "MG94xREV with separate rates for branch sets":0.005257318382466263,
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iuc
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190 "Nucleotide GTR":0.005093980037543817,
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iuc
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191 "constrained":0.005312488930776041,
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iuc
parents:
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192 "original name":"gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human",
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iuc
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193 "unconstrained":0.005310237663772852
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iuc
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194 },
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iuc
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195 "gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human":{
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iuc
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196 "MG94xREV with separate rates for branch sets":0.003479916215861459,
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iuc
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197 "Nucleotide GTR":0.003379296026417724,
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iuc
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198 "constrained":0.00346850100589682,
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iuc
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diff changeset
199 "original name":"gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human",
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iuc
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200 "unconstrained":0.003467075173450572
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iuc
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201 },
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iuc
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diff changeset
202 "gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human":{
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iuc
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203 "MG94xREV with separate rates for branch sets":0.003464849064657331,
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iuc
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204 "Nucleotide GTR":0.003372774424630234,
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iuc
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205 "constrained":0.003509522487583494,
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iuc
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diff changeset
206 "original name":"gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human",
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iuc
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diff changeset
207 "unconstrained":0.003508106640264412
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iuc
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208 },
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iuc
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diff changeset
209 "gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human":{
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iuc
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210 "MG94xREV with separate rates for branch sets":0.003473329346287882,
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iuc
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diff changeset
211 "Nucleotide GTR":0.003374190595560375,
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iuc
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diff changeset
212 "constrained":0.003460491667549116,
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iuc
parents:
diff changeset
213 "original name":"gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human",
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iuc
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diff changeset
214 "unconstrained":0.003458961168696655
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iuc
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diff changeset
215 },
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iuc
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diff changeset
216 "gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human":{
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iuc
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218 "Nucleotide GTR":0.00505933790460295,
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iuc
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diff changeset
219 "constrained":0.005212676662201692,
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iuc
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diff changeset
220 "original name":"gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human",
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iuc
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221 "unconstrained":0.00521043198515884
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iuc
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diff changeset
222 },
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iuc
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diff changeset
223 "gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human":{
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iuc
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225 "Nucleotide GTR":0.003373764235314068,
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iuc
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diff changeset
226 "constrained":0.003487667486541674,
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iuc
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diff changeset
227 "original name":"gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human",
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iuc
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228 "unconstrained":0.003486166370330776
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iuc
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229 },
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iuc
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diff changeset
230 "gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human":{
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iuc
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232 "Nucleotide GTR":0.005068409188375663,
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iuc
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diff changeset
233 "constrained":0.005291926605586965,
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iuc
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diff changeset
234 "original name":"gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human",
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iuc
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235 "unconstrained":0.005289677385186297
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iuc
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diff changeset
236 },
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iuc
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diff changeset
237 "gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human":{
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238 "MG94xREV with separate rates for branch sets":0.003464842721698225,
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iuc
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239 "Nucleotide GTR":0.003372774424770855,
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iuc
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diff changeset
240 "constrained":0.003508044185651234,
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iuc
parents:
diff changeset
241 "original name":"gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human",
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iuc
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242 "unconstrained":0.003507815553802554
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iuc
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243 },
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iuc
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diff changeset
244 "gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human":{
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iuc
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246 "Nucleotide GTR":0.001686266012390882,
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iuc
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diff changeset
247 "constrained":0.001736374314870017,
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iuc
parents:
diff changeset
248 "original name":"gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human",
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iuc
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249 "unconstrained":0.001735532172102446
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iuc
parents:
diff changeset
250 },
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iuc
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diff changeset
251 "gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human":{
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252 "MG94xREV with separate rates for branch sets":0.003480097445970276,
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iuc
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253 "Nucleotide GTR":0.003374436490976879,
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iuc
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diff changeset
254 "constrained":0.003479100177235689,
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iuc
parents:
diff changeset
255 "original name":"gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human",
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iuc
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diff changeset
256 "unconstrained":0.003478891730919581
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iuc
parents:
diff changeset
257 },
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iuc
parents:
diff changeset
258 "gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human":{
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iuc
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259 "MG94xREV with separate rates for branch sets":0.00347257104743095,
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iuc
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260 "Nucleotide GTR":0.003376034743011948,
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iuc
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diff changeset
261 "constrained":0.003518997887784842,
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iuc
parents:
diff changeset
262 "original name":"gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human",
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iuc
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263 "unconstrained":0.003517561264776653
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iuc
parents:
diff changeset
264 },
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iuc
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diff changeset
265 "gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human":{
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266 "MG94xREV with separate rates for branch sets":0.003474988463675508,
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iuc
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267 "Nucleotide GTR":0.003374190741831846,
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iuc
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diff changeset
268 "constrained":0.003517174184123671,
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iuc
parents:
diff changeset
269 "original name":"gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human",
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iuc
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270 "unconstrained":0.00351929009659662
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iuc
parents:
diff changeset
271 },
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iuc
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diff changeset
272 "gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human":{
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273 "MG94xREV with separate rates for branch sets":0.003471294880555319,
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iuc
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274 "Nucleotide GTR":0.003376937492543959,
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iuc
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275 "constrained":0.003517915599429177,
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iuc
parents:
diff changeset
276 "original name":"gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human",
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iuc
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277 "unconstrained":0.003516462270783854
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iuc
parents:
diff changeset
278 }
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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279 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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diff changeset
280 "attributes":{
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iuc
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281 "MG94xREV with separate rates for branch sets":{
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iuc
parents:
diff changeset
282 "attribute type":"branch length",
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iuc
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diff changeset
283 "display order":1
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iuc
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284 },
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iuc
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diff changeset
285 "Nucleotide GTR":{
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iuc
parents:
diff changeset
286 "attribute type":"branch length",
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
287 "display order":0
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iuc
parents:
diff changeset
288 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
289 "constrained":{
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iuc
parents:
diff changeset
290 "attribute type":"branch length",
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iuc
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diff changeset
291 "display order":1
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iuc
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diff changeset
292 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
293 "original name":{
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iuc
parents:
diff changeset
294 "attribute type":"node label",
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iuc
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diff changeset
295 "display order":0
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iuc
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diff changeset
296 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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diff changeset
297 "unconstrained":{
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iuc
parents:
diff changeset
298 "attribute type":"branch length",
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iuc
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diff changeset
299 "display order":0
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iuc
parents:
diff changeset
300 }
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iuc
parents:
diff changeset
301 }
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iuc
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diff changeset
302 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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diff changeset
303 "data partitions":{
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iuc
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diff changeset
304 "0":{
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iuc
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diff changeset
305 "coverage": [
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
306 [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197]
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
307 ],
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
308 "name":"busted.filter.default"
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
309 }
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
310 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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diff changeset
311 "fits":{
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iuc
parents:
diff changeset
312 "Constrained model":{
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iuc
parents:
diff changeset
313 "AIC-c":2537.370055580011,
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iuc
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diff changeset
314 "Log Likelihood":-1205.042170647148,
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
315 "Rate Distributions":{
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iuc
parents:
diff changeset
316 "Background":{
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iuc
parents:
diff changeset
317 "0":{
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iuc
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diff changeset
318 "omega":0.00623371489168318,
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iuc
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diff changeset
319 "proportion":0.02824597255703105
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iuc
parents:
diff changeset
320 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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diff changeset
321 "1":{
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iuc
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diff changeset
322 "omega":0.1719986773053319,
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iuc
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diff changeset
323 "proportion":0.8104926399157489
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iuc
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diff changeset
324 },
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iuc
parents:
diff changeset
325 "2":{
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iuc
parents:
diff changeset
326 "omega":2.233103409549535,
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iuc
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diff changeset
327 "proportion":0.16126138752722
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
328 }
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
329 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
330 "Synonymous site-to-site rates":{
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iuc
parents:
diff changeset
331 "0":{
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iuc
parents:
diff changeset
332 "proportion":0,
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
333 "rate":0.9507923294014373
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
334 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
335 "1":{
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iuc
parents:
diff changeset
336 "proportion":1,
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iuc
parents:
diff changeset
337 "rate":1
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
338 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
339 "2":{
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iuc
parents:
diff changeset
340 "proportion":0,
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
341 "rate":1.059005087778388
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
342 }
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
343 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
344 "Test":{
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
345 "0":{
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iuc
parents:
diff changeset
346 "omega":0.9993683385761363,
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
347 "proportion":2.155223602575912e-10
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
348 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
349 "1":{
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iuc
parents:
diff changeset
350 "omega":0.999707726011995,
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iuc
parents:
diff changeset
351 "proportion":2.155223602111413e-10
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
352 },
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iuc
parents:
diff changeset
353 "2":{
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iuc
parents:
diff changeset
354 "omega":1,
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
355 "proportion":0.9999999995689552
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iuc
parents:
diff changeset
356 }
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
357 }
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
358 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
359 "display order":3,
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
360 "estimated parameters":63
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iuc
parents:
diff changeset
361 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
362 "MG94xREV with separate rates for branch sets":{
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iuc
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diff changeset
363 "AIC-c":2512.962001126987,
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iuc
parents:
diff changeset
364 "Equilibrium frequencies": [
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iuc
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diff changeset
365 [0.03825952761243274],
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366 [0.01370948533169502],
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367 [0.0238326285579188],
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iuc
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426 ],
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427 "Log Likelihood":-1205.058976375078,
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428 "Rate Distributions":{
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429 "non-synonymous/synonymous rate ratio for *background*": [
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431 ],
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432 "non-synonymous/synonymous rate ratio for *test*": [
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434 ]
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435 },
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436 "display order":1,
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437 "estimated parameters":51
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438 },
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439 "Nucleotide GTR":{
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440 "AIC-c":2633.0046471406,
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441 "Equilibrium frequencies": [
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446 ],
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447 "Log Likelihood":-1247.247280799152,
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448 "Rate Distributions":{
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diff changeset
449 "Substitution rate from nucleotide A to nucleotide C":0,
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diff changeset
450 "Substitution rate from nucleotide A to nucleotide G":1,
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diff changeset
451 "Substitution rate from nucleotide A to nucleotide T":0.3101631549852981,
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iuc
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diff changeset
452 "Substitution rate from nucleotide C to nucleotide G":1.129990583516242,
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453 "Substitution rate from nucleotide C to nucleotide T":2.723444388603395,
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diff changeset
454 "Substitution rate from nucleotide G to nucleotide T":1.720896006888861
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455 },
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diff changeset
456 "display order":0,
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457 "estimated parameters":69
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diff changeset
458 },
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diff changeset
459 "Unconstrained model":{
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diff changeset
460 "AIC-c":2538.426858070025,
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iuc
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diff changeset
461 "Log Likelihood":-1204.550057961818,
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iuc
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diff changeset
462 "Rate Distributions":{
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iuc
parents:
diff changeset
463 "Background":{
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466 "proportion":0.02741862862724963
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472 "2":{
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473 "omega":2.232058479326601,
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474 "proportion":0.1613986842363778
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475 }
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477 "Synonymous site-to-site rates":{
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478 "0":{
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479 "proportion":0,
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480 "rate":0.9502886367487763
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482 "1":{
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483 "proportion":1,
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484 "rate":1
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485 },
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486 "2":{
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487 "proportion":0,
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488 "rate":1.059678592887729
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489 }
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490 },
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iuc
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491 "Test":{
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492 "0":{
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493 "omega":0.9993684330797956,
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494 "proportion":0
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495 },
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496 "1":{
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497 "omega":0.999368433118802,
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498 "proportion":0
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499 },
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500 "2":{
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501 "omega":25.32658549655282,
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502 "proportion":1
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503 }
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iuc
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504 }
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iuc
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505 },
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iuc
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506 "display order":2,
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iuc
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507 "estimated parameters":64
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508 }
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iuc
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509 },
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iuc
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510 "input":{
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511 "file name":"/home/aglucaci/SARS-CoV-2/clades/B-1-617/nsp8.combined.fas",
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iuc
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diff changeset
512 "number of sequences":32,
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iuc
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diff changeset
513 "number of sites":198,
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iuc
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514 "partition count":1,
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iuc
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515 "trees":{
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iuc
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diff changeset
516 "0":"(REFERENCE,(gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human,epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021)Node20,gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human,epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021,(epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021,gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human)Node4,epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021,gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human,gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human,epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021,gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human,(gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human,gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human,epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021)Node38,epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021,gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human,epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021,gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human,epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021,epi_isl_1543980_hCoV_19_Singapore_490_2021,epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021,gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human,epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021,gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human,gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human,epi_isl_1652118_hCoV_19_Singapore_575_2021,epi_isl_1652105_hCoV_19_Singapore_561_2021,gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human,gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human,epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021,epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021)"
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
517 }
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iuc
parents:
diff changeset
518 },
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iuc
parents:
diff changeset
519 "test results":{
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iuc
parents:
diff changeset
520 "LRT":0.9842253706597148,
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iuc
parents:
diff changeset
521 "p-value":0.3056667368082906
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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522 },
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iuc
parents:
diff changeset
523 "tested":{
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iuc
parents:
diff changeset
524 "0":{
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iuc
parents:
diff changeset
525 "Node20":"test",
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iuc
parents:
diff changeset
526 "Node38":"background",
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
527 "Node4":"test",
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
528 "REFERENCE":"background",
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
529 "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":"background",
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iuc
parents:
diff changeset
530 "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":"background",
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
531 "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":"background",
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
532 "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":"background",
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
533 "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":"background",
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
534 "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":"background",
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
535 "epi_isl_1543980_hCoV_19_Singapore_490_2021":"background",
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
536 "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":"background",
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
537 "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":"background",
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
538 "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":"background",
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iuc
parents:
diff changeset
539 "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":"background",
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
540 "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":"background",
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
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c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
542 "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":"background",
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iuc
parents:
diff changeset
543 "epi_isl_1652105_hCoV_19_Singapore_561_2021":"background",
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
544 "epi_isl_1652118_hCoV_19_Singapore_575_2021":"background",
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
545 "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":"background",
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iuc
parents:
diff changeset
546 "gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human":"background",
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iuc
parents:
diff changeset
547 "gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human":"background",
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iuc
parents:
diff changeset
548 "gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human":"background",
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
549 "gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human":"background",
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iuc
parents:
diff changeset
550 "gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human":"background",
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
551 "gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human":"background",
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
552 "gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human":"background",
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
553 "gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human":"background",
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
554 "gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human":"background",
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
555 "gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human":"background",
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
556 "gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human":"background",
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
557 "gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human":"background",
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
558 "gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human":"background",
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
559 "gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human":"background"
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
560 }
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
561 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
562 "timers":{
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
563 "Constrained BUSTED model fitting":{
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
564 "order":3,
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
565 "timer":3
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
566 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
567 "Overall":{
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
568 "order":0,
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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diff changeset
569 "timer":76
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iuc
parents:
diff changeset
570 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
571 "Preliminary model fitting":{
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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diff changeset
572 "order":1,
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iuc
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diff changeset
573 "timer":6
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iuc
parents:
diff changeset
574 },
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
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diff changeset
575 "Unconstrained BUSTED model fitting":{
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iuc
parents:
diff changeset
576 "order":2,
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iuc
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diff changeset
577 "timer":66
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iuc
parents:
diff changeset
578 }
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
579 }
c046f72e5e3a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
iuc
parents:
diff changeset
580 }