{"sha": "3f065dbdd4e1ea1f2e623d3c6431b35210dcfed5", "data": {"nexml": {"@about": "#study", "@generator": "Open Tree API", "@id": "study", "@nexml2json": "1.2.1", "@nexmljson": "http://purl.org/opentree/nexson", "@version": "0.9", "@xmlns": {"$": "http://www.nexml.org/2009", "nex": "http://www.nexml.org/2009", "ot": "http://purl.org/opentree-terms#", "xhtml": "http://www.w3.org/1999/xhtml/vocab#", "xsd": "http://www.w3.org/2001/XMLSchema#", "xsi": "http://www.w3.org/2001/XMLSchema-instance"}, "^ot:agents": {"agent": [{"@description": "Open Tree NexSON validation", "@id": "peyotl-validator", "@name": "api.opentreeoflife.org/validate", "@url": "https://github.com/OpenTreeOfLife/peyotl", "@version": "0.0.4a", "invocation": {"commandLine": [], "otherProperty": [{"name": "pythonVersion", "value": "2.7.9"}, {"name": "pythonImplementation", "value": "CPython"}]}}, {"@description": "Web-based interface for submitting, editing, and reviewing studies in the Open Tree of Life project.", "@id": "opentree-curation-webapp", "@name": "OpenTree curation webapp", "@url": "https://github.com/OpenTreeOfLife/opentree", "@version": "0.0.0"}]}, "^ot:annotationEvents": {"annotation": [{"@dateCreated": "2015-07-08T20:47:26.490Z", "@description": "Aids for mapping study OTUs to OTT taxa", "@id": "otu-mapping-hints", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "OTU_MAPPING_HINTS", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"searchContext": {"$": "Bacteria"}, "substitutions": {"substitution": [{"@active": false, "@valid": true, "new": {"$": ""}, "old": {"$": ""}}]}, "useFuzzyMatching": false}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@dateCreated": "2015-07-08T20:47:26.490Z", "@description": "Describes supporting data files for this study", "@id": "supporting-files-metadata", "@passedChecks": true, "@preserve": true, "@wasAssociatedWithAgentId": "opentree-curation-webapp", "message": [{"@code": "SUPPORTING_FILE_INFO", "@humanMessageType": "NONE", "@severity": "INFO", "data": {"@movedToPermanentArchive": false, "files": {"file": [{"@filename": "PASTED.tre", "@size": 447, "@type": "newick", "@url": "/curator/download/supporting_files.doc.9c80b16d3975d2f4.5041535445442e747265.tre", "description": {"$": "Source data for tree(s) 'tree1'"}, "sourceForTree": [{"$": "tree1"}]}, {"@filename": "ListeriaMono_LyveSet.tre", "@size": 1840, "@type": "newick", "@url": "/curator/download/supporting_files.doc.a480e22ff9b5b541.4c697374657269614d6f6e6f5f4c7976655365742e747265.tre", "description": {"$": "Source data for tree(s) 'tree2'"}, "sourceForTree": [{"$": "tree2"}]}, {"@filename": "E.coli_MLTree.txt", "@size": 547, "@type": "newick", "@url": "/curator/download/supporting_files.doc.b073d061cd7724f3.452e636f6c695f4d4c547265652e747874.txt", "description": {"$": "Source data for tree(s) 'tree3'"}, "sourceForTree": [{"$": "tree3"}]}, {"@filename": "SIM-Sbareilly.tre", "@size": 384, "@type": "newick", "@url": "/curator/download/supporting_files.doc.8fba6ba119b6c6d3.53494d2d5362617265696c6c792e747265.tre", "description": {"$": "Source data for tree(s) 'tree4'"}, "sourceForTree": [{"$": "tree4"}]}, {"@filename": "PASTED.tre", "@size": 1089, "@type": "newick", "@url": "/curator/download/supporting_files.doc.820296e5457bf9a4.5041535445442e747265.tre", "description": {"$": "Source data for tree(s) 'tree8'"}, "sourceForTree": [{"$": "tree8"}]}]}}, "refersTo": {"@top": {"$": "meta"}}}]}, {"@id": "peyotl-validator-event", "@description": "Open Tree NexSON validation", "@wasAssociatedWithAgentId": "peyotl-validator", "@passedChecks": true, "@preserve": false, "message": [{"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge100", "@treesID": "trees1", "@treeID": "tree3", "@edgeID": "edge100"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge32", "@treesID": "trees1", "@treeID": "tree2", "@edgeID": "edge32"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge33", "@treesID": "trees1", "@treeID": "tree2", "@edgeID": "edge33"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge34", "@treesID": "trees1", "@treeID": "tree2", "@edgeID": "edge34"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge35", "@treesID": "trees1", "@treeID": "tree2", "@edgeID": "edge35"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge37", "@treesID": "trees1", "@treeID": "tree2", "@edgeID": "edge37"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge39", "@treesID": "trees1", "@treeID": "tree2", "@edgeID": "edge39"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge41", "@treesID": "trees1", "@treeID": "tree2", "@edgeID": "edge41"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge44", "@treesID": "trees1", "@treeID": "tree2", "@edgeID": "edge44"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge45", "@treesID": "trees1", "@treeID": "tree2", "@edgeID": "edge45"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge48", "@treesID": "trees1", "@treeID": "tree2", "@edgeID": "edge48"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge50", "@treesID": "trees1", "@treeID": "tree2", "@edgeID": "edge50"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge52", "@treesID": "trees1", "@treeID": "tree2", "@edgeID": "edge52"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge53", "@treesID": "trees1", "@treeID": "tree2", "@edgeID": "edge53"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge56", "@treesID": "trees1", "@treeID": "tree2", "@edgeID": "edge56"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge57", "@treesID": "trees1", "@treeID": "tree2", "@edgeID": "edge57"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge59", "@treesID": "trees1", "@treeID": "tree2", "@edgeID": "edge59"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge62", "@treesID": "trees1", "@treeID": "tree2", "@edgeID": "edge62"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge65", "@treesID": "trees1", "@treeID": "tree2", "@edgeID": "edge65"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge66", "@treesID": "trees1", "@treeID": "tree2", "@edgeID": "edge66"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge67", "@treesID": "trees1", "@treeID": "tree2", "@edgeID": "edge67"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge71", "@treesID": "trees1", "@treeID": "tree2", "@edgeID": "edge71"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge72", "@treesID": "trees1", "@treeID": "tree2", "@edgeID": "edge72"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge76", "@treesID": "trees1", "@treeID": "tree2", "@edgeID": "edge76"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge78", "@treesID": "trees1", "@treeID": "tree2", "@edgeID": "edge78"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge80", "@treesID": "trees1", "@treeID": "tree2", "@edgeID": "edge80"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge82", "@treesID": "trees1", "@treeID": "tree2", "@edgeID": "edge82"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge83", "@treesID": "trees1", "@treeID": "tree2", "@edgeID": "edge83"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge88", "@treesID": "trees1", "@treeID": "tree3", "@edgeID": "edge88"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge89", "@treesID": "trees1", "@treeID": "tree3", "@edgeID": "edge89"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge93", "@treesID": "trees1", "@treeID": "tree3", "@edgeID": "edge93"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge95", "@treesID": "trees1", "@treeID": "tree3", "@edgeID": "edge95"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge97", "@treesID": "trees1", "@treeID": "tree3", "@edgeID": "edge97"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:bootstrapValues"], "refersTo": {"@top": "trees", "@idref": "edge98", "@treesID": "trees1", "@treeID": "tree3", "@edgeID": "edge98"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node102", "@treesID": "trees1", "@treeID": "tree3", "@nodeID": "node102"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node104", "@treesID": "trees1", "@treeID": "tree3", "@nodeID": "node104"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node105", "@treesID": "trees1", "@treeID": "tree3", "@nodeID": "node105"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node106", "@treesID": "trees1", "@treeID": "tree3", "@nodeID": "node106"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node11", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node11"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node111", "@treesID": "trees1", "@treeID": "tree4", "@nodeID": "node111"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node112", "@treesID": "trees1", "@treeID": "tree4", "@nodeID": "node112"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node114", "@treesID": "trees1", "@treeID": "tree4", "@nodeID": "node114"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node115", "@treesID": "trees1", "@treeID": "tree4", "@nodeID": "node115"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node116", "@treesID": "trees1", "@treeID": "tree4", "@nodeID": "node116"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node118", "@treesID": "trees1", "@treeID": "tree4", "@nodeID": "node118"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node12", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node12"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node120", "@treesID": "trees1", "@treeID": "tree4", "@nodeID": "node120"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node121", "@treesID": "trees1", "@treeID": "tree4", "@nodeID": "node121"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node122", "@treesID": "trees1", "@treeID": "tree4", "@nodeID": "node122"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node123", "@treesID": "trees1", "@treeID": "tree4", "@nodeID": "node123"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node124", "@treesID": "trees1", "@treeID": "tree4", "@nodeID": "node124"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node125", "@treesID": "trees1", "@treeID": "tree4", "@nodeID": "node125"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node126", "@treesID": "trees1", "@treeID": "tree4", "@nodeID": "node126"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node127", "@treesID": "trees1", "@treeID": "tree4", "@nodeID": "node127"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node128", "@treesID": "trees1", "@treeID": "tree4", "@nodeID": "node128"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node129", "@treesID": "trees1", "@treeID": "tree4", "@nodeID": "node129"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node13", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node13"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node130", "@treesID": "trees1", "@treeID": "tree4", "@nodeID": "node130"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node131", "@treesID": "trees1", "@treeID": "tree4", "@nodeID": "node131"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node132", "@treesID": "trees1", "@treeID": "tree4", "@nodeID": "node132"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node133", "@treesID": "trees1", "@treeID": "tree4", "@nodeID": "node133"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node134", "@treesID": "trees1", "@treeID": "tree4", "@nodeID": "node134"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node135", "@treesID": "trees1", "@treeID": "tree4", "@nodeID": "node135"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node136", "@treesID": "trees1", "@treeID": "tree4", "@nodeID": "node136"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node14", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node14"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node15", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node15"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node16", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node16"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node17", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node17"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node18", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node18"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node19", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node19"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node20", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node20"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node21", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node21"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node22", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node22"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node23", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node23"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node24", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node24"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node25", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node25"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node26", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node26"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node27", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node27"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node28", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node28"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node29", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node29"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node31", "@treesID": "trees1", "@treeID": "tree2", "@nodeID": "node31"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["@label"], "refersTo": {"@top": "trees", "@idref": "node32", "@treesID": "trees1", "@treeID": "tree2", "@nodeID": "node32"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node33", "@treesID": "trees1", "@treeID": "tree2", "@nodeID": "node33"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node38", "@treesID": "trees1", "@treeID": "tree2", "@nodeID": "node38"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node4", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node4"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node40", "@treesID": "trees1", "@treeID": "tree2", "@nodeID": "node40"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node42", "@treesID": "trees1", "@treeID": "tree2", "@nodeID": "node42"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node44", "@treesID": "trees1", "@treeID": "tree2", "@nodeID": "node44"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node45", "@treesID": "trees1", "@treeID": "tree2", "@nodeID": "node45"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node48", "@treesID": "trees1", "@treeID": "tree2", "@nodeID": "node48"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node49", "@treesID": "trees1", "@treeID": "tree2", "@nodeID": "node49"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node5", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node5"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node51", "@treesID": "trees1", "@treeID": "tree2", "@nodeID": "node51"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node53", "@treesID": "trees1", "@treeID": "tree2", "@nodeID": "node53"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node56", "@treesID": "trees1", "@treeID": "tree2", "@nodeID": "node56"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node57", "@treesID": "trees1", "@treeID": "tree2", "@nodeID": "node57"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node60", "@treesID": "trees1", "@treeID": "tree2", "@nodeID": "node60"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node62", "@treesID": "trees1", "@treeID": "tree2", "@nodeID": "node62"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node63", "@treesID": "trees1", "@treeID": "tree2", "@nodeID": "node63"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node65", "@treesID": "trees1", "@treeID": "tree2", "@nodeID": "node65"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node66", "@treesID": "trees1", "@treeID": "tree2", "@nodeID": "node66"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node7", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node7"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node70", "@treesID": "trees1", "@treeID": "tree2", "@nodeID": "node70"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node71", "@treesID": "trees1", "@treeID": "tree2", "@nodeID": "node71"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node72", "@treesID": "trees1", "@treeID": "tree2", "@nodeID": "node72"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node75", "@treesID": "trees1", "@treeID": "tree2", "@nodeID": "node75"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node76", "@treesID": "trees1", "@treeID": "tree2", "@nodeID": "node76"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node77", "@treesID": "trees1", "@treeID": "tree2", "@nodeID": "node77"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node79", "@treesID": "trees1", "@treeID": "tree2", "@nodeID": "node79"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node8", "@treesID": "trees1", "@treeID": "tree1", "@nodeID": "node8"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node81", "@treesID": "trees1", "@treeID": "tree2", "@nodeID": "node81"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node83", "@treesID": "trees1", "@treeID": "tree2", "@nodeID": "node83"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node86", "@treesID": "trees1", "@treeID": "tree2", "@nodeID": "node86"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node87", "@treesID": "trees1", "@treeID": "tree2", "@nodeID": "node87"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node88", "@treesID": "trees1", "@treeID": "tree2", "@nodeID": "node88"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node89", "@treesID": "trees1", "@treeID": "tree2", "@nodeID": "node89"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node93", "@treesID": "trees1", "@treeID": "tree3", "@nodeID": "node93"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node94", "@treesID": "trees1", "@treeID": "tree3", "@nodeID": "node94"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node95", "@treesID": "trees1", "@treeID": "tree3", "@nodeID": "node95"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node97", "@treesID": "trees1", "@treeID": "tree3", "@nodeID": "node97"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:isTaxonExemplar"], "refersTo": {"@top": "trees", "@idref": "node99", "@treesID": "trees1", "@treeID": "tree3", "@nodeID": "node99"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu1", "otu10", "otu11", "otu12", "otu13", "otu14", "otu15", "otu16", "otu17", "otu18", "otu19", "otu2", "otu20", "otu21", "otu22", "otu23", "otu3", "otu4", "otu5", "otu6", "otu7", "otu8", "otu9"], "refersTo": {"@top": "otus", "@idref": "otus1", "@otusID": "otus1"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu100", "otu101", "otu102", "otu103", "otu104", "otu105", "otu106", "otu107", "otu108", "otu109", "otu110", "otu111", "otu112", "otu91", "otu92", "otu93", "otu94", "otu95", "otu96", "otu97", "otu98", "otu99"], "refersTo": {"@top": "otus", "@idref": "otus1", "@otusID": "otus1"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu24", "otu25", "otu26", "otu27", "otu28", "otu29", "otu30", "otu31", "otu32", "otu33", "otu34", "otu35", "otu36", "otu37", "otu38", "otu39", "otu40", "otu41", "otu42", "otu43", "otu44", "otu45", "otu46", "otu47", "otu48", "otu49", "otu50", "otu51", "otu52", "otu53", "otu54"], "refersTo": {"@top": "otus", "@idref": "otus1", "@otusID": "otus1"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu55", "otu56", "otu58", "otu59"], "refersTo": {"@top": "otus", "@idref": "otus1", "@otusID": "otus1"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu57", "otu60", "otu61", "otu62", "otu63"], "refersTo": {"@top": "otus", "@idref": "otus1", "@otusID": "otus1"}, "@severity": "WARNING"}, {"@code": "MULTIPLE_TIPS_MAPPED_TO_OTT_ID", "data": ["otu65", "otu66", "otu67", "otu68", "otu69", "otu70", "otu71", "otu72", "otu73", "otu74", "otu75", "otu76", "otu77", "otu78", "otu79", "otu80", "otu81", "otu82", "otu83", "otu84", "otu85", "otu86", "otu87"], "refersTo": {"@top": "otus", "@idref": "otus1", "@otusID": "otus1"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:comment"], "refersTo": {"@top": "nexml", "@idref": "study"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:nodeLabelMode", "^ot:nodeLabelTimeUnit", "^ot:reasonsToExcludeFromSynthesis"], "refersTo": {"@top": "trees", "@idref": "tree1", "@treesID": "trees1", "@treeID": "tree1"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:nodeLabelDescription", "^ot:nodeLabelMode", "^ot:nodeLabelTimeUnit", "^ot:reasonsToExcludeFromSynthesis"], "refersTo": {"@top": "trees", "@idref": "tree2", "@treesID": "trees1", "@treeID": "tree2"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:nodeLabelDescription", "^ot:nodeLabelMode", "^ot:nodeLabelTimeUnit", "^ot:reasonsToExcludeFromSynthesis"], "refersTo": {"@top": "trees", "@idref": "tree3", "@treesID": "trees1", "@treeID": "tree3"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:nodeLabelMode", "^ot:nodeLabelTimeUnit", "^ot:reasonsToExcludeFromSynthesis"], "refersTo": {"@top": "trees", "@idref": "tree4", "@treesID": "trees1", "@treeID": "tree4"}, "@severity": "WARNING"}, {"@code": "UNRECOGNIZED_KEY", "data": ["^ot:nodeLabelMode", "^ot:nodeLabelTimeUnit", "^ot:reasonsToExcludeFromSynthesis"], "refersTo": {"@top": "trees", "@idref": "tree8", "@treesID": "trees1", "@treeID": "tree8"}, "@severity": "WARNING"}]}]}, "^ot:candidateTreeForSynthesis": ["tree1", "tree2", "tree3", "tree4"], "^ot:comment": "", "^ot:curatorName": ["Ruth Timme"], "^ot:dataDeposit": {"@href": "https://github.com/WGS-standards-and-analysis/datasets"}, "^ot:focalClade": 844192, "^ot:focalCladeOTTTaxonName": "Bacteria (domain in cellular organisms)", "^ot:otusElementOrder": ["otus1"], "^ot:studyId": "ot_301", "^ot:studyPublication": {"@href": "https://peerj.com/articles/3893"}, "^ot:studyPublicationReference": "Ruth E Timme, Hugh Rand, Martin Shumway, Eija K Trees, Mustafa Simmons, Richa Agarwala, Steven Davis, Glen Tillman, Stephanie Defibaugh-Chavez, Heather A Carleton, William A Klimke, Lee S Katz, 2017, 'Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance'", "^ot:studyYear": 2017, "^ot:tag": ["foodborne outbreak", "SNP phylogeny"], "^ot:treesElementOrder": ["trees1"], "^xhtml:license": {"@href": "http://creativecommons.org/publicdomain/zero/1.0/"}, "otusById": {"otus1": {"otuById": {"otu1": {"^ot:originalLabel": "CFSAN000211", "^ot:ottId": 739160, "^ot:ottTaxonName": "Salmonella enterica subsp. enterica serovar Bareilly"}, "otu10": {"^ot:originalLabel": "CFSAN000954", "^ot:ottId": 739160, "^ot:ottTaxonName": "Salmonella enterica subsp. enterica serovar Bareilly"}, "otu100": {"^ot:originalLabel": "D7328", "^ot:ottId": 559439, "^ot:ottTaxonName": "Campylobacter jejuni"}, "otu101": {"^ot:originalLabel": "D7320", "^ot:ottId": 559439, "^ot:ottTaxonName": "Campylobacter jejuni"}, "otu102": {"^ot:originalLabel": "D7331", "^ot:ottId": 559439, "^ot:ottTaxonName": "Campylobacter jejuni"}, "otu103": {"^ot:originalLabel": "D7321", "^ot:ottId": 559439, "^ot:ottTaxonName": "Campylobacter jejuni"}, "otu104": {"^ot:originalLabel": "D7329", "^ot:ottId": 559439, "^ot:ottTaxonName": "Campylobacter jejuni"}, "otu105": {"^ot:originalLabel": "2014D-0067", "^ot:ottId": 559439, "^ot:ottTaxonName": "Campylobacter jejuni"}, "otu106": {"^ot:originalLabel": "2014D-0070", "^ot:ottId": 559439, "^ot:ottTaxonName": "Campylobacter jejuni"}, "otu107": {"^ot:originalLabel": "2014D-0189", "^ot:ottId": 559439, "^ot:ottTaxonName": "Campylobacter jejuni"}, "otu108": {"^ot:originalLabel": "2014D-0068", "^ot:ottId": 559439, "^ot:ottTaxonName": "Campylobacter jejuni"}, "otu109": {"^ot:originalLabel": "D5663", "^ot:ottId": 559439, "^ot:ottTaxonName": "Campylobacter jejuni"}, "otu11": {"^ot:originalLabel": "CFSAN000963", "^ot:ottId": 739160, "^ot:ottTaxonName": "Salmonella enterica subsp. enterica serovar Bareilly"}, "otu110": {"^ot:originalLabel": "PNUSA000195", "^ot:ottId": 559439, "^ot:ottTaxonName": "Campylobacter jejuni"}, "otu111": {"^ot:originalLabel": "PNUSA000196", "^ot:ottId": 559439, "^ot:ottTaxonName": "Campylobacter jejuni"}, "otu112": {"^ot:originalLabel": "PNUSA000194", "^ot:ottId": 559439, "^ot:ottTaxonName": "Campylobacter jejuni"}, "otu12": {"^ot:originalLabel": "CFSAN000958", "^ot:ottId": 739160, "^ot:ottTaxonName": "Salmonella enterica subsp. enterica serovar Bareilly"}, "otu13": {"^ot:originalLabel": "CFSAN000951", "^ot:ottId": 739160, "^ot:ottTaxonName": "Salmonella enterica subsp. enterica serovar Bareilly"}, "otu14": {"^ot:originalLabel": "CFSAN001118", "^ot:ottId": 739160, "^ot:ottTaxonName": "Salmonella enterica subsp. enterica serovar Bareilly"}, "otu15": {"^ot:originalLabel": "CFSAN000700", "^ot:ottId": 739160, "^ot:ottTaxonName": "Salmonella enterica subsp. enterica serovar Bareilly"}, "otu16": {"^ot:originalLabel": "CFSAN001115", "^ot:ottId": 739160, "^ot:ottTaxonName": "Salmonella enterica subsp. enterica serovar Bareilly"}, "otu17": {"^ot:originalLabel": "CFSAN000752", "^ot:ottId": 739160, "^ot:ottTaxonName": "Salmonella enterica subsp. enterica serovar Bareilly"}, "otu18": {"^ot:originalLabel": "CFSAN000669", "^ot:ottId": 739160, "^ot:ottTaxonName": "Salmonella enterica subsp. enterica serovar Bareilly"}, "otu19": {"^ot:originalLabel": "CFSAN000970", "^ot:ottId": 739160, "^ot:ottTaxonName": "Salmonella enterica subsp. enterica serovar Bareilly"}, "otu2": {"^ot:originalLabel": "CFSAN000212", "^ot:ottId": 739160, "^ot:ottTaxonName": "Salmonella enterica subsp. enterica serovar Bareilly"}, "otu20": {"^ot:originalLabel": "CFSAN001112", "^ot:ottId": 739160, "^ot:ottTaxonName": "Salmonella enterica subsp. enterica serovar Bareilly"}, "otu21": {"^ot:originalLabel": "CFSAN000753", "^ot:ottId": 739160, "^ot:ottTaxonName": "Salmonella enterica subsp. enterica serovar Bareilly"}, "otu22": {"^ot:originalLabel": "CFSAN000961", "^ot:ottId": 739160, "^ot:ottTaxonName": "Salmonella enterica subsp. enterica serovar Bareilly"}, "otu23": {"^ot:originalLabel": "CFSAN000189", "^ot:ottId": 739160, "^ot:ottTaxonName": "Salmonella enterica subsp. enterica serovar Bareilly"}, "otu24": {"^ot:originalLabel": "CFSAN002349", "^ot:ottId": 1038312, "^ot:ottTaxonName": "Listeria monocytogenes"}, "otu25": {"^ot:originalLabel": "PNUSAL000957", "^ot:ottId": 1038312, "^ot:ottTaxonName": "Listeria monocytogenes"}, "otu26": {"^ot:originalLabel": "MOD1 LS985", "^ot:ottId": 1038312, "^ot:ottTaxonName": "Listeria monocytogenes"}, "otu27": {"^ot:originalLabel": "CFSAN023464", "^ot:ottId": 1038312, "^ot:ottTaxonName": "Listeria monocytogenes"}, "otu28": {"^ot:originalLabel": "CFSAN023465", "^ot:ottId": 1038312, "^ot:ottTaxonName": "Listeria monocytogenes"}, "otu29": {"^ot:originalLabel": "CFSAN023471", "^ot:ottId": 1038312, "^ot:ottTaxonName": "Listeria monocytogenes"}, "otu3": {"^ot:originalLabel": "CFSAN000191", "^ot:ottId": 739160, "^ot:ottTaxonName": "Salmonella enterica subsp. enterica serovar Bareilly"}, "otu30": {"^ot:originalLabel": "CFSAN023470", "^ot:ottId": 1038312, "^ot:ottTaxonName": "Listeria monocytogenes"}, "otu31": {"^ot:originalLabel": "MOD1 LS997", "^ot:ottId": 1038312, "^ot:ottTaxonName": "Listeria monocytogenes"}, "otu32": {"^ot:originalLabel": "MOD1 LS1011", "^ot:ottId": 1038312, "^ot:ottTaxonName": "Listeria monocytogenes"}, "otu33": {"^ot:originalLabel": "MOD1 LS1003", "^ot:ottId": 1038312, "^ot:ottTaxonName": "Listeria monocytogenes"}, "otu34": {"^ot:originalLabel": "MOD1 LS1009", "^ot:ottId": 1038312, "^ot:ottTaxonName": "Listeria monocytogenes"}, "otu35": {"^ot:originalLabel": "MOD1 LS1006", "^ot:ottId": 1038312, "^ot:ottTaxonName": "Listeria monocytogenes"}, "otu36": {"^ot:originalLabel": "MOD1 LS989", "^ot:ottId": 1038312, "^ot:ottTaxonName": "Listeria monocytogenes"}, "otu37": {"^ot:originalLabel": "MOD1 LS1010", "^ot:ottId": 1038312, "^ot:ottTaxonName": "Listeria monocytogenes"}, "otu38": {"^ot:originalLabel": "MOD1 LS996", "^ot:ottId": 1038312, "^ot:ottTaxonName": "Listeria monocytogenes"}, "otu39": {"^ot:originalLabel": "MOD1 LS998", "^ot:ottId": 1038312, "^ot:ottTaxonName": "Listeria monocytogenes"}, "otu4": {"^ot:originalLabel": "CFSAN000228", "^ot:ottId": 739160, "^ot:ottTaxonName": "Salmonella enterica subsp. enterica serovar Bareilly"}, "otu40": {"^ot:originalLabel": "MOD1 LS1004", "^ot:ottId": 1038312, "^ot:ottTaxonName": "Listeria monocytogenes"}, "otu41": {"^ot:originalLabel": "MOD1 LS994", "^ot:ottId": 1038312, "^ot:ottTaxonName": "Listeria monocytogenes"}, "otu42": {"^ot:originalLabel": "CFSAN023468", "^ot:ottId": 1038312, "^ot:ottTaxonName": "Listeria monocytogenes"}, "otu43": {"^ot:originalLabel": "MOD1 LS1008", "^ot:ottId": 1038312, "^ot:ottTaxonName": "Listeria monocytogenes"}, "otu44": {"^ot:originalLabel": "CFSAN023469", "^ot:ottId": 1038312, "^ot:ottTaxonName": "Listeria monocytogenes"}, "otu45": {"^ot:originalLabel": "CFSAN023463", "^ot:ottId": 1038312, "^ot:ottTaxonName": "Listeria monocytogenes"}, "otu46": {"^ot:originalLabel": "MOD1 LS982", "^ot:ottId": 1038312, "^ot:ottTaxonName": "Listeria monocytogenes"}, "otu47": {"^ot:originalLabel": "PNUSAL000870", "^ot:ottId": 1038312, "^ot:ottTaxonName": "Listeria monocytogenes"}, "otu48": {"^ot:originalLabel": "PNUSAL001024", "^ot:ottId": 1038312, "^ot:ottTaxonName": "Listeria monocytogenes"}, "otu49": {"^ot:originalLabel": "MOD1 LS995", "^ot:ottId": 1038312, "^ot:ottTaxonName": "Listeria monocytogenes"}, "otu5": {"^ot:originalLabel": "CFSAN000661", "^ot:ottId": 739160, "^ot:ottTaxonName": "Salmonella enterica subsp. enterica serovar Bareilly"}, "otu50": {"^ot:originalLabel": "MOD1 LS1005", "^ot:ottId": 1038312, "^ot:ottTaxonName": "Listeria monocytogenes"}, "otu51": {"^ot:originalLabel": "MOD1 LS1000", "^ot:ottId": 1038312, "^ot:ottTaxonName": "Listeria monocytogenes"}, "otu52": {"^ot:originalLabel": "CFSAN023466", "^ot:ottId": 1038312, "^ot:ottTaxonName": "Listeria monocytogenes"}, "otu53": {"^ot:originalLabel": "CFSAN023467", "^ot:ottId": 1038312, "^ot:ottTaxonName": "Listeria monocytogenes"}, "otu54": {"^ot:originalLabel": "PNUSAL000730", "^ot:ottId": 1038312, "^ot:ottTaxonName": "Listeria monocytogenes"}, "otu55": {"^ot:originalLabel": "2014C-3655", "^ot:ottId": 5341889, "^ot:ottTaxonName": "Escherichia coli"}, "otu56": {"^ot:originalLabel": "2014C-3656", "^ot:ottId": 5341889, "^ot:ottTaxonName": "Escherichia coli"}, "otu57": {"^ot:originalLabel": "2014C-3907", "^ot:ottId": 5251867, "^ot:ottTaxonName": "Escherichia coli"}, "otu58": {"^ot:originalLabel": "2011C-3609.fasta.wgsim", "^ot:ottId": 5341889, "^ot:ottTaxonName": "Escherichia coli"}, "otu59": {"^ot:originalLabel": "2014C-3857", "^ot:ottId": 5341889, "^ot:ottTaxonName": "Escherichia coli"}, "otu6": {"^ot:originalLabel": "CFSAN001140", "^ot:ottId": 739160, "^ot:ottTaxonName": "Salmonella enterica subsp. enterica serovar Bareilly"}, "otu60": {"^ot:originalLabel": "2014C-3598", "^ot:ottId": 5251867, "^ot:ottTaxonName": "Escherichia coli"}, "otu61": {"^ot:originalLabel": "2014C-3600", "^ot:ottId": 5251867, "^ot:ottTaxonName": "Escherichia coli"}, "otu62": {"^ot:originalLabel": "2014C-3599", "^ot:ottId": 5251867, "^ot:ottTaxonName": "Escherichia coli"}, "otu63": {"^ot:originalLabel": "2014C-3850", "^ot:ottId": 5251867, "^ot:ottTaxonName": "Escherichia coli"}, "otu64": {"^ot:originalLabel": "2014C-3840", "^ot:ottId": 5251870, "^ot:ottTaxonName": "Escherichia coli"}, "otu65": {"^ot:originalLabel": "SIM 000211", "^ot:ottId": 338023, "^ot:ottTaxonName": "Salmonella enterica (merged with Salmonella)"}, "otu66": {"^ot:originalLabel": "SIM 000212", "^ot:ottId": 338023, "^ot:ottTaxonName": "Salmonella enterica (merged with Salmonella)"}, "otu67": {"^ot:originalLabel": "SIM 000191", "^ot:ottId": 338023, "^ot:ottTaxonName": "Salmonella enterica (merged with Salmonella)"}, "otu68": {"^ot:originalLabel": "SIM 000228", "^ot:ottId": 338023, "^ot:ottTaxonName": "Salmonella enterica (merged with Salmonella)"}, "otu69": {"^ot:originalLabel": "SIM 000189", "^ot:ottId": 338023, "^ot:ottTaxonName": "Salmonella enterica (merged with Salmonella)"}, "otu7": {"^ot:originalLabel": "CFSAN000968", "^ot:ottId": 739160, "^ot:ottTaxonName": "Salmonella enterica subsp. enterica serovar Bareilly"}, "otu70": {"^ot:originalLabel": "SIM 000961", "^ot:ottId": 338023, "^ot:ottTaxonName": "Salmonella enterica (merged with Salmonella)"}, "otu71": {"^ot:originalLabel": "SIM 000661", "^ot:ottId": 338023, "^ot:ottTaxonName": "Salmonella enterica (merged with Salmonella)"}, "otu72": {"^ot:originalLabel": "SIM 001140", "^ot:ottId": 338023, "^ot:ottTaxonName": "Salmonella enterica (merged with Salmonella)"}, "otu73": {"^ot:originalLabel": "SIM 000968", "^ot:ottId": 338023, "^ot:ottTaxonName": "Salmonella enterica (merged with Salmonella)"}, "otu74": {"^ot:originalLabel": "SIM 000960", "^ot:ottId": 338023, "^ot:ottTaxonName": "Salmonella enterica (merged with Salmonella)"}, "otu75": {"^ot:originalLabel": "SIM 000952", "^ot:ottId": 338023, "^ot:ottTaxonName": "Salmonella enterica (merged with Salmonella)"}, "otu76": {"^ot:originalLabel": "SIM 000954", "^ot:ottId": 338023, "^ot:ottTaxonName": "Salmonella enterica (merged with Salmonella)"}, "otu77": {"^ot:originalLabel": "SIM 000963", "^ot:ottId": 338023, "^ot:ottTaxonName": "Salmonella enterica (merged with Salmonella)"}, "otu78": {"^ot:originalLabel": "SIM 000958", "^ot:ottId": 338023, "^ot:ottTaxonName": "Salmonella enterica (merged with Salmonella)"}, "otu79": {"^ot:originalLabel": "SIM 000951", "^ot:ottId": 338023, "^ot:ottTaxonName": "Salmonella enterica (merged with Salmonella)"}, "otu8": {"^ot:originalLabel": "CFSAN000960", "^ot:ottId": 739160, "^ot:ottTaxonName": "Salmonella enterica subsp. enterica serovar Bareilly"}, "otu80": {"^ot:originalLabel": "SIM 001118", "^ot:ottId": 338023, "^ot:ottTaxonName": "Salmonella enterica (merged with Salmonella)"}, "otu81": {"^ot:originalLabel": "SIM 000700", "^ot:ottId": 338023, "^ot:ottTaxonName": "Salmonella enterica (merged with Salmonella)"}, "otu82": {"^ot:originalLabel": "SIM 001115", "^ot:ottId": 338023, "^ot:ottTaxonName": "Salmonella enterica (merged with Salmonella)"}, "otu83": {"^ot:originalLabel": "SIM 000752", "^ot:ottId": 338023, "^ot:ottTaxonName": "Salmonella enterica (merged with Salmonella)"}, "otu84": {"^ot:originalLabel": "SIM 000669", "^ot:ottId": 338023, "^ot:ottTaxonName": "Salmonella enterica (merged with Salmonella)"}, "otu85": {"^ot:originalLabel": "SIM 000970", "^ot:ottId": 338023, "^ot:ottTaxonName": "Salmonella enterica (merged with Salmonella)"}, "otu86": {"^ot:originalLabel": "SIM 001112", "^ot:ottId": 338023, "^ot:ottTaxonName": "Salmonella enterica (merged with Salmonella)"}, "otu87": {"^ot:originalLabel": "SIM 000753", "^ot:ottId": 338023, "^ot:ottTaxonName": "Salmonella enterica (merged with Salmonella)"}, "otu9": {"^ot:originalLabel": "CFSAN000952", "^ot:ottId": 739160, "^ot:ottTaxonName": "Salmonella enterica subsp. enterica serovar Bareilly"}, "otu91": {"^ot:originalLabel": "D7324", "^ot:ottId": 559439, "^ot:ottTaxonName": "Campylobacter jejuni"}, "otu92": {"^ot:originalLabel": "D7316", "^ot:ottId": 559439, "^ot:ottTaxonName": "Campylobacter jejuni"}, "otu93": {"^ot:originalLabel": "D7333", "^ot:ottId": 559439, "^ot:ottTaxonName": "Campylobacter jejuni"}, "otu94": {"^ot:originalLabel": "D7334", "^ot:ottId": 559439, "^ot:ottTaxonName": "Campylobacter jejuni"}, "otu95": {"^ot:originalLabel": "D7319", "^ot:ottId": 559439, "^ot:ottTaxonName": "Campylobacter jejuni"}, "otu96": {"^ot:originalLabel": "D7323", "^ot:ottId": 559439, "^ot:ottTaxonName": "Campylobacter jejuni"}, "otu97": {"^ot:originalLabel": "D7327", "^ot:ottId": 559439, "^ot:ottTaxonName": "Campylobacter jejuni"}, "otu98": {"^ot:originalLabel": "D7330", "^ot:ottId": 559439, "^ot:ottTaxonName": "Campylobacter jejuni"}, "otu99": {"^ot:originalLabel": "D7322", "^ot:ottId": 559439, "^ot:ottTaxonName": "Campylobacter jejuni"}}}}, "treesById": {"trees1": {"@otus": "otus1", "^ot:treeElementOrder": ["tree1", "tree2", "tree3", "tree4", "tree8"], "treeById": {"tree1": {"@label": "SalBareilly.tre", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "ot:undefined", "^ot:branchLengthTimeUnit": "Myr", "^ot:curatedType": "Maximum likelihood ", "^ot:inGroupClade": "node9", "^ot:nodeLabelMode": "", "^ot:nodeLabelTimeUnit": "", "^ot:outGroupEdge": "", "^ot:reasonsToExcludeFromSynthesis": [], "^ot:rootNodeId": "node1", "^ot:specifiedRoot": "node1", "^ot:tag": [], "^ot:unrootedTree": false, "edgeBySourceId": {"node1": {"edge1": {"@length": 0.931185, "@source": "node1", "@target": "node2"}, "edge28": {"@length": 0, "@source": "node1", "@target": "node29"}, "edge8": {"@length": 0.158186, "@source": "node1", "@target": "node9"}}, "node10": {"edge10": {"@length": 0, "@source": "node10", "@target": "node11"}, "edge11": {"@length": 0, "@source": "node10", "@target": "node12"}, "edge12": {"@length": 0, "@source": "node10", "@target": "node13"}, "edge13": {"@length": 0, "@source": "node10", "@target": "node14"}, "edge14": {"@length": 0, "@source": "node10", "@target": "node15"}, "edge15": {"@length": 0, "@source": "node10", "@target": "node16"}, "edge16": {"@length": 0, "@source": "node10", "@target": "node17"}, "edge17": {"@length": 0, "@source": "node10", "@target": "node18"}, "edge18": {"@length": 0, "@source": "node10", "@target": "node19"}, "edge19": {"@length": 0, "@source": "node10", "@target": "node20"}, "edge20": {"@length": 0.006604, "@source": "node10", "@target": "node21"}, "edge21": {"@length": 0, "@source": "node10", "@target": "node22"}, "edge22": {"@length": 0, "@source": "node10", "@target": "node23"}, "edge23": {"@length": 0, "@source": "node10", "@target": "node24"}, "edge24": {"@length": 0, "@source": "node10", "@target": "node25"}, "edge25": {"@length": 0, "@source": "node10", "@target": "node26"}, "edge26": {"@length": 0, "@source": "node10", "@target": "node27"}}, "node2": {"edge2": {"@length": 0.475086, "@source": "node2", "@target": "node3"}, "edge5": {"@length": 0.021467, "@source": "node2", "@target": "node6"}}, "node3": {"edge3": {"@length": 0, "@source": "node3", "@target": "node4"}, "edge4": {"@length": 0.006844, "@source": "node3", "@target": "node5"}}, "node6": {"edge6": {"@length": 0.184402, "@source": "node6", "@target": "node7"}, "edge7": {"@length": 0.059318, "@source": "node6", "@target": "node8"}}, "node9": {"edge27": {"@length": 0, "@source": "node9", "@target": "node28"}, "edge9": {"@length": 0.006609, "@source": "node9", "@target": "node10"}}}, "nodeById": {"node1": {"@root": true}, "node10": {}, "node11": {"@otu": "otu5", "^ot:isTaxonExemplar": false}, "node12": {"@otu": "otu6", "^ot:isTaxonExemplar": false}, "node13": {"@otu": "otu7", "^ot:isTaxonExemplar": false}, "node14": {"@otu": "otu8", "^ot:isTaxonExemplar": false}, "node15": {"@otu": "otu9", "^ot:isTaxonExemplar": false}, "node16": {"@otu": "otu10", "^ot:isTaxonExemplar": false}, "node17": {"@otu": "otu11", "^ot:isTaxonExemplar": false}, "node18": {"@otu": "otu12", "^ot:isTaxonExemplar": false}, "node19": {"@otu": "otu13", "^ot:isTaxonExemplar": false}, "node2": {}, "node20": {"@otu": "otu14", "^ot:isTaxonExemplar": false}, "node21": {"@otu": "otu15", "^ot:isTaxonExemplar": false}, "node22": {"@otu": "otu16", "^ot:isTaxonExemplar": false}, "node23": {"@otu": "otu17", "^ot:isTaxonExemplar": false}, "node24": {"@otu": "otu18", "^ot:isTaxonExemplar": false}, "node25": {"@otu": "otu19", "^ot:isTaxonExemplar": false}, "node26": {"@otu": "otu20", "^ot:isTaxonExemplar": false}, "node27": {"@otu": "otu21", "^ot:isTaxonExemplar": false}, "node28": {"@otu": "otu22", "^ot:isTaxonExemplar": false}, "node29": {"@otu": "otu23", "^ot:isTaxonExemplar": true}, "node3": {}, "node4": {"@otu": "otu1", "^ot:isTaxonExemplar": false}, "node5": {"@otu": "otu2", "^ot:isTaxonExemplar": false}, "node6": {}, "node7": {"@otu": "otu3", "^ot:isTaxonExemplar": false}, "node8": {"@otu": "otu4", "^ot:isTaxonExemplar": false}, "node9": {}}}, "tree2": {"@label": "Listeria_monocytogenes.tre", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "ot:undefined", "^ot:branchLengthTimeUnit": "Myr", "^ot:curatedType": "Maximum likelihood ", "^ot:inGroupClade": "node34", "^ot:nodeLabelDescription": "", "^ot:nodeLabelMode": "ot:bootstrapValues", "^ot:nodeLabelTimeUnit": "", "^ot:outGroupEdge": "", "^ot:reasonsToExcludeFromSynthesis": [], "^ot:rootNodeId": "node32", "^ot:specifiedRoot": "node32", "^ot:tag": [], "^ot:unrootedTree": false, "edgeBySourceId": {"node30": {"edge29": {"@length": 0.016497, "@source": "node30", "@target": "node31"}, "edge87": {"@length": 0.027771, "@source": "node30", "@target": "node89"}}, "node32": {"edge30": {"@length": 0.005009, "@source": "node32", "@target": "node30"}, "edge31": {"@length": 0.010343, "@source": "node32", "@target": "node33"}, "edge32": {"@length": 0.005639, "@source": "node32", "@target": "node34", "^ot:bootstrapValues": 100}}, "node34": {"edge33": {"@length": 0.010363, "@source": "node34", "@target": "node35", "^ot:bootstrapValues": 100}, "edge76": {"@length": 0.012765, "@source": "node34", "@target": "node78", "^ot:bootstrapValues": 100}}, "node35": {"edge34": {"@length": 0.003039, "@source": "node35", "@target": "node36", "^ot:bootstrapValues": 100}, "edge65": {"@length": 0.001176, "@source": "node35", "@target": "node67", "^ot:bootstrapValues": 96}}, "node36": {"edge35": {"@length": 0.001201, "@source": "node36", "@target": "node37", "^ot:bootstrapValues": 96}, "edge44": {"@length": 1e-06, "@source": "node36", "@target": "node46", "^ot:bootstrapValues": 28}}, "node37": {"edge36": {"@length": 0.000602, "@source": "node37", "@target": "node38"}, "edge37": {"@length": 1e-06, "@source": "node37", "@target": "node39", "^ot:bootstrapValues": 43}}, "node39": {"edge38": {"@length": 1e-06, "@source": "node39", "@target": "node40"}, "edge39": {"@length": 1e-06, "@source": "node39", "@target": "node41", "^ot:bootstrapValues": 30}}, "node41": {"edge40": {"@length": 1e-06, "@source": "node41", "@target": "node42"}, "edge41": {"@length": 1e-06, "@source": "node41", "@target": "node43", "^ot:bootstrapValues": 67}}, "node43": {"edge42": {"@length": 1e-06, "@source": "node43", "@target": "node44"}, "edge43": {"@length": 1e-06, "@source": "node43", "@target": "node45"}}, "node46": {"edge45": {"@length": 0.000601, "@source": "node46", "@target": "node47", "^ot:bootstrapValues": 79}, "edge48": {"@length": 1e-06, "@source": "node46", "@target": "node50", "^ot:bootstrapValues": 23}}, "node47": {"edge46": {"@length": 0.000601, "@source": "node47", "@target": "node48"}, "edge47": {"@length": 1e-06, "@source": "node47", "@target": "node49"}}, "node50": {"edge49": {"@length": 1e-06, "@source": "node50", "@target": "node51"}, "edge50": {"@length": 1e-06, "@source": "node50", "@target": "node52", "^ot:bootstrapValues": 4}}, "node52": {"edge51": {"@length": 1e-06, "@source": "node52", "@target": "node53"}, "edge52": {"@length": 1e-06, "@source": "node52", "@target": "node54", "^ot:bootstrapValues": 16}}, "node54": {"edge53": {"@length": 1e-06, "@source": "node54", "@target": "node55", "^ot:bootstrapValues": 36}, "edge56": {"@length": 1e-06, "@source": "node54", "@target": "node58", "^ot:bootstrapValues": 2}}, "node55": {"edge54": {"@length": 1e-06, "@source": "node55", "@target": "node56"}, "edge55": {"@length": 1e-06, "@source": "node55", "@target": "node57"}}, "node58": {"edge57": {"@length": 1e-06, "@source": "node58", "@target": "node59", "^ot:bootstrapValues": 1}, "edge62": {"@length": 1e-06, "@source": "node58", "@target": "node64", "^ot:bootstrapValues": 58}}, "node59": {"edge58": {"@length": 1e-06, "@source": "node59", "@target": "node60"}, "edge59": {"@length": 1e-06, "@source": "node59", "@target": "node61", "^ot:bootstrapValues": 1}}, "node61": {"edge60": {"@length": 1e-06, "@source": "node61", "@target": "node62"}, "edge61": {"@length": 0.000603, "@source": "node61", "@target": "node63"}}, "node64": {"edge63": {"@length": 1e-06, "@source": "node64", "@target": "node65"}, "edge64": {"@length": 1e-06, "@source": "node64", "@target": "node66"}}, "node67": {"edge66": {"@length": 1e-06, "@source": "node67", "@target": "node68", "^ot:bootstrapValues": 45}, "edge71": {"@length": 1e-06, "@source": "node67", "@target": "node73", "^ot:bootstrapValues": 49}}, "node68": {"edge67": {"@length": 1e-06, "@source": "node68", "@target": "node69", "^ot:bootstrapValues": 41}, "edge70": {"@length": 0.000603, "@source": "node68", "@target": "node72"}}, "node69": {"edge68": {"@length": 1e-06, "@source": "node69", "@target": "node70"}, "edge69": {"@length": 1e-06, "@source": "node69", "@target": "node71"}}, "node73": {"edge72": {"@length": 1e-06, "@source": "node73", "@target": "node74", "^ot:bootstrapValues": 20}, "edge75": {"@length": 1e-06, "@source": "node73", "@target": "node77"}}, "node74": {"edge73": {"@length": 0.0006, "@source": "node74", "@target": "node75"}, "edge74": {"@length": 0.0006, "@source": "node74", "@target": "node76"}}, "node78": {"edge77": {"@length": 1e-06, "@source": "node78", "@target": "node79"}, "edge78": {"@length": 1e-06, "@source": "node78", "@target": "node80", "^ot:bootstrapValues": 75}}, "node80": {"edge79": {"@length": 1e-06, "@source": "node80", "@target": "node81"}, "edge80": {"@length": 1e-06, "@source": "node80", "@target": "node82", "^ot:bootstrapValues": 46}}, "node82": {"edge81": {"@length": 1e-06, "@source": "node82", "@target": "node83"}, "edge82": {"@length": 1e-06, "@source": "node82", "@target": "node84", "^ot:bootstrapValues": 45}}, "node84": {"edge83": {"@length": 0.002999, "@source": "node84", "@target": "node85", "^ot:bootstrapValues": 71}, "edge86": {"@length": 0.000603, "@source": "node84", "@target": "node88"}}, "node85": {"edge84": {"@length": 1e-06, "@source": "node85", "@target": "node86"}, "edge85": {"@length": 0.000602, "@source": "node85", "@target": "node87"}}}, "nodeById": {"node30": {}, "node31": {"@otu": "otu24", "^ot:isTaxonExemplar": false}, "node32": {"@label": "100", "@root": true}, "node33": {"@otu": "otu25", "^ot:isTaxonExemplar": false}, "node34": {}, "node35": {}, "node36": {}, "node37": {}, "node38": {"@otu": "otu26", "^ot:isTaxonExemplar": false}, "node39": {}, "node40": {"@otu": "otu27", "^ot:isTaxonExemplar": false}, "node41": {}, "node42": {"@otu": "otu28", "^ot:isTaxonExemplar": false}, "node43": {}, "node44": {"@otu": "otu29", "^ot:isTaxonExemplar": false}, "node45": {"@otu": "otu30", "^ot:isTaxonExemplar": false}, "node46": {}, "node47": {}, "node48": {"@otu": "otu31", "^ot:isTaxonExemplar": false}, "node49": {"@otu": "otu32", "^ot:isTaxonExemplar": false}, "node50": {}, "node51": {"@otu": "otu33", "^ot:isTaxonExemplar": false}, "node52": {}, "node53": {"@otu": "otu34", "^ot:isTaxonExemplar": false}, "node54": {}, "node55": {}, "node56": {"@otu": "otu35", "^ot:isTaxonExemplar": false}, "node57": {"@otu": "otu36", "^ot:isTaxonExemplar": false}, "node58": {}, "node59": {}, "node60": {"@otu": "otu37", "^ot:isTaxonExemplar": false}, "node61": {}, "node62": {"@otu": "otu38", "^ot:isTaxonExemplar": false}, "node63": {"@otu": "otu39", "^ot:isTaxonExemplar": false}, "node64": {}, "node65": {"@otu": "otu40", "^ot:isTaxonExemplar": false}, "node66": {"@otu": "otu41", "^ot:isTaxonExemplar": false}, "node67": {}, "node68": {}, "node69": {}, "node70": {"@otu": "otu42", "^ot:isTaxonExemplar": false}, "node71": {"@otu": "otu43", "^ot:isTaxonExemplar": false}, "node72": {"@otu": "otu44", "^ot:isTaxonExemplar": false}, "node73": {}, "node74": {}, "node75": {"@otu": "otu45", "^ot:isTaxonExemplar": false}, "node76": {"@otu": "otu46", "^ot:isTaxonExemplar": false}, "node77": {"@otu": "otu47", "^ot:isTaxonExemplar": true}, "node78": {}, "node79": {"@otu": "otu48", "^ot:isTaxonExemplar": false}, "node80": {}, "node81": {"@otu": "otu49", "^ot:isTaxonExemplar": false}, "node82": {}, "node83": {"@otu": "otu50", "^ot:isTaxonExemplar": false}, "node84": {}, "node85": {}, "node86": {"@otu": "otu51", "^ot:isTaxonExemplar": false}, "node87": {"@otu": "otu52", "^ot:isTaxonExemplar": false}, "node88": {"@otu": "otu53", "^ot:isTaxonExemplar": false}, "node89": {"@otu": "otu54", "^ot:isTaxonExemplar": false}}}, "tree3": {"@label": "Escherichia_coli.tre", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "ot:undefined", "^ot:branchLengthTimeUnit": "Myr", "^ot:curatedType": "Maximum likelihood ", "^ot:inGroupClade": "", "^ot:nodeLabelDescription": "", "^ot:nodeLabelMode": "ot:bootstrapValues", "^ot:nodeLabelTimeUnit": "", "^ot:outGroupEdge": "", "^ot:reasonsToExcludeFromSynthesis": [], "^ot:rootNodeId": "node90", "^ot:specifiedRoot": "node90", "^ot:tag": [], "^ot:unrootedTree": false, "edgeBySourceId": {"node100": {"edge103": {"@length": 0.006336, "@source": "node100", "@target": "node106"}, "edge98": {"@length": 0.007183, "@source": "node100", "@target": "node101", "^ot:bootstrapValues": 100}}, "node101": {"edge100": {"@length": 1e-06, "@source": "node101", "@target": "node103", "^ot:bootstrapValues": 63}, "edge99": {"@length": 1e-06, "@source": "node101", "@target": "node102"}}, "node103": {"edge101": {"@length": 0.000705, "@source": "node103", "@target": "node104"}, "edge102": {"@length": 9.7e-05, "@source": "node103", "@target": "node105"}}, "node90": {"edge104": {"@length": 0.010773, "@source": "node90", "@target": "node107"}, "edge88": {"@length": 0.000918, "@source": "node90", "@target": "node91", "^ot:bootstrapValues": 100}, "edge93": {"@length": 0.002352, "@source": "node90", "@target": "node96", "^ot:bootstrapValues": 100}}, "node91": {"edge89": {"@length": 0.007715, "@source": "node91", "@target": "node92", "^ot:bootstrapValues": 100}, "edge92": {"@length": 0.013671, "@source": "node91", "@target": "node95"}}, "node92": {"edge90": {"@length": 9.5e-05, "@source": "node92", "@target": "node93"}, "edge91": {"@length": 0.000999, "@source": "node92", "@target": "node94"}}, "node96": {"edge94": {"@length": 0.007325, "@source": "node96", "@target": "node97"}, "edge95": {"@length": 0.000377, "@source": "node96", "@target": "node98", "^ot:bootstrapValues": 67}}, "node98": {"edge96": {"@length": 0.007638, "@source": "node98", "@target": "node99"}, "edge97": {"@length": 1e-06, "@source": "node98", "@target": "node100", "^ot:bootstrapValues": 32}}}, "nodeById": {"node100": {}, "node101": {}, "node102": {"@otu": "otu60", "^ot:isTaxonExemplar": false}, "node103": {}, "node104": {"@otu": "otu61", "^ot:isTaxonExemplar": true}, "node105": {"@otu": "otu62", "^ot:isTaxonExemplar": false}, "node106": {"@otu": "otu63", "^ot:isTaxonExemplar": false}, "node107": {"@otu": "otu64"}, "node90": {"@root": true}, "node91": {}, "node92": {}, "node93": {"@otu": "otu55", "^ot:isTaxonExemplar": false}, "node94": {"@otu": "otu56", "^ot:isTaxonExemplar": false}, "node95": {"@otu": "otu57", "^ot:isTaxonExemplar": false}, "node96": {}, "node97": {"@otu": "otu58", "^ot:isTaxonExemplar": false}, "node98": {}, "node99": {"@otu": "otu59", "^ot:isTaxonExemplar": true}}}, "tree4": {"@label": "Simulated-SalBareilly.tre", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "ot:substitutionCount", "^ot:branchLengthTimeUnit": "", "^ot:curatedType": "Maximum likelihood ", "^ot:inGroupClade": "node119", "^ot:nodeLabelMode": "", "^ot:nodeLabelTimeUnit": "", "^ot:outGroupEdge": "", "^ot:reasonsToExcludeFromSynthesis": [], "^ot:rootNodeId": "tree4_ROOT", "^ot:specifiedRoot": "tree4_ROOT", "^ot:tag": [], "^ot:unrootedTree": false, "edgeBySourceId": {"node108": {"edge105": {"@length": 0.931185, "@source": "node108", "@target": "node109"}, "edge112": {"@length": 0, "@source": "node108", "@target": "node116"}}, "node109": {"edge106": {"@length": 0.475086, "@source": "node109", "@target": "node110"}, "edge109": {"@length": 0.021467, "@source": "node109", "@target": "node113"}}, "node110": {"edge107": {"@length": 0, "@source": "node110", "@target": "node111"}, "edge108": {"@length": 0.006844, "@source": "node110", "@target": "node112"}}, "node113": {"edge110": {"@length": 0.184402, "@source": "node113", "@target": "node114"}, "edge111": {"@length": 0.059318, "@source": "node113", "@target": "node115"}}, "node117": {"edge114": {"@length": 0, "@source": "node117", "@target": "node118"}, "edge115": {"@length": 0.006609, "@source": "node117", "@target": "node119"}}, "node119": {"edge116": {"@length": 0, "@source": "node119", "@target": "node120"}, "edge117": {"@length": 0, "@source": "node119", "@target": "node121"}, "edge118": {"@length": 0, "@source": "node119", "@target": "node122"}, "edge119": {"@length": 0, "@source": "node119", "@target": "node123"}, "edge120": {"@length": 0, "@source": "node119", "@target": "node124"}, "edge121": {"@length": 0, "@source": "node119", "@target": "node125"}, "edge122": {"@length": 0, "@source": "node119", "@target": "node126"}, "edge123": {"@length": 0, "@source": "node119", "@target": "node127"}, "edge124": {"@length": 0, "@source": "node119", "@target": "node128"}, "edge125": {"@length": 0, "@source": "node119", "@target": "node129"}, "edge126": {"@length": 0.006604, "@source": "node119", "@target": "node130"}, "edge127": {"@length": 0, "@source": "node119", "@target": "node131"}, "edge128": {"@length": 0, "@source": "node119", "@target": "node132"}, "edge129": {"@length": 0, "@source": "node119", "@target": "node133"}, "edge130": {"@length": 0, "@source": "node119", "@target": "node134"}, "edge131": {"@length": 0, "@source": "node119", "@target": "node135"}, "edge132": {"@length": 0, "@source": "node119", "@target": "node136"}}, "tree4_ROOT": {"edge113": {"@length": 0.158186, "@source": "tree4_ROOT", "@target": "node108"}, "tree4_ROOT_EDGE": {"@source": "tree4_ROOT", "@target": "node117"}}}, "nodeById": {"node108": {}, "node109": {}, "node110": {}, "node111": {"@otu": "otu65", "^ot:isTaxonExemplar": true}, "node112": {"@otu": "otu66", "^ot:isTaxonExemplar": false}, "node113": {}, "node114": {"@otu": "otu67", "^ot:isTaxonExemplar": false}, "node115": {"@otu": "otu68", "^ot:isTaxonExemplar": false}, "node116": {"@otu": "otu69", "^ot:isTaxonExemplar": false}, "node117": {}, "node118": {"@otu": "otu70", "^ot:isTaxonExemplar": false}, "node119": {}, "node120": {"@otu": "otu71", "^ot:isTaxonExemplar": false}, "node121": {"@otu": "otu72", "^ot:isTaxonExemplar": false}, "node122": {"@otu": "otu73", "^ot:isTaxonExemplar": false}, "node123": {"@otu": "otu74", "^ot:isTaxonExemplar": false}, "node124": {"@otu": "otu75", "^ot:isTaxonExemplar": false}, "node125": {"@otu": "otu76", "^ot:isTaxonExemplar": false}, "node126": {"@otu": "otu77", "^ot:isTaxonExemplar": false}, "node127": {"@otu": "otu78", "^ot:isTaxonExemplar": false}, "node128": {"@otu": "otu79", "^ot:isTaxonExemplar": false}, "node129": {"@otu": "otu80", "^ot:isTaxonExemplar": false}, "node130": {"@otu": "otu81", "^ot:isTaxonExemplar": false}, "node131": {"@otu": "otu82", "^ot:isTaxonExemplar": false}, "node132": {"@otu": "otu83", "^ot:isTaxonExemplar": false}, "node133": {"@otu": "otu84", "^ot:isTaxonExemplar": false}, "node134": {"@otu": "otu85", "^ot:isTaxonExemplar": false}, "node135": {"@otu": "otu86", "^ot:isTaxonExemplar": false}, "node136": {"@otu": "otu87", "^ot:isTaxonExemplar": false}, "tree4_ROOT": {"@root": true}}}, "tree8": {"@label": "campylobacter_jejuni.tre", "@xsi:type": "nex:FloatTree", "^ot:branchLengthDescription": "", "^ot:branchLengthMode": "ot:bootstrapValues", "^ot:branchLengthTimeUnit": "", "^ot:curatedType": "Maximum likelihood ", "^ot:inGroupClade": "node142", "^ot:nodeLabelMode": "", "^ot:nodeLabelTimeUnit": "", "^ot:outGroupEdge": "", "^ot:reasonsToExcludeFromSynthesis": [], "^ot:rootNodeId": "node140", "^ot:specifiedRoot": "node140", "^ot:tag": [], "^ot:unrootedTree": false, "edgeBySourceId": {"node140": {"edge136": {"@length": 0.012006, "@source": "node140", "@target": "node141"}, "edge171": {"@length": 0.012007, "@source": "node140", "@target": "node176"}}, "node141": {"edge137": {"@length": 0.313701, "@source": "node141", "@target": "node142"}, "edge164": {"@length": 0.322621, "@source": "node141", "@target": "node169"}}, "node142": {"edge138": {"@length": 1e-06, "@source": "node142", "@target": "node143"}, "edge139": {"@length": 0.011528, "@source": "node142", "@target": "node144"}}, "node144": {"edge140": {"@length": 1e-06, "@source": "node144", "@target": "node145"}, "edge163": {"@length": 0.00072, "@source": "node144", "@target": "node168"}}, "node145": {"edge141": {"@length": 1e-06, "@source": "node145", "@target": "node146"}, "edge142": {"@length": 0.012203, "@source": "node145", "@target": "node147"}}, "node147": {"edge143": {"@length": 1e-06, "@source": "node147", "@target": "node148"}, "edge156": {"@length": 0.008451, "@source": "node147", "@target": "node161"}}, "node148": {"edge144": {"@length": 1e-06, "@source": "node148", "@target": "node149"}, "edge147": {"@length": 1e-06, "@source": "node148", "@target": "node152"}}, "node149": {"edge145": {"@length": 1e-06, "@source": "node149", "@target": "node150"}, "edge146": {"@length": 1e-06, "@source": "node149", "@target": "node151"}}, "node152": {"edge148": {"@length": 1e-06, "@source": "node152", "@target": "node153"}, "edge155": {"@length": 1e-06, "@source": "node152", "@target": "node160"}}, "node153": {"edge149": {"@length": 0.01145, "@source": "node153", "@target": "node154"}, "edge154": {"@length": 1e-06, "@source": "node153", "@target": "node159"}}, "node154": {"edge150": {"@length": 1e-06, "@source": "node154", "@target": "node155"}, "edge153": {"@length": 1e-06, "@source": "node154", "@target": "node158"}}, "node155": {"edge151": {"@length": 0.001423, "@source": "node155", "@target": "node156"}, "edge152": {"@length": 1e-06, "@source": "node155", "@target": "node157"}}, "node161": {"edge157": {"@length": 0.002726, "@source": "node161", "@target": "node162"}, "edge162": {"@length": 1e-06, "@source": "node161", "@target": "node167"}}, "node162": {"edge158": {"@length": 0.000678, "@source": "node162", "@target": "node163"}, "edge159": {"@length": 0.01705, "@source": "node162", "@target": "node164"}}, "node164": {"edge160": {"@length": 0.000832, "@source": "node164", "@target": "node165"}, "edge161": {"@length": 0.00119, "@source": "node164", "@target": "node166"}}, "node169": {"edge165": {"@length": 1e-06, "@source": "node169", "@target": "node170"}, "edge166": {"@length": 0.003237, "@source": "node169", "@target": "node171"}}, "node171": {"edge167": {"@length": 1e-06, "@source": "node171", "@target": "node172"}, "edge168": {"@length": 1e-06, "@source": "node171", "@target": "node173"}}, "node173": {"edge169": {"@length": 1e-06, "@source": "node173", "@target": "node174"}, "edge170": {"@length": 1e-06, "@source": "node173", "@target": "node175"}}, "node176": {"edge172": {"@length": 0.24993, "@source": "node176", "@target": "node177"}, "edge173": {"@length": 0.201507, "@source": "node176", "@target": "node178"}}, "node178": {"edge174": {"@length": 0.001489, "@source": "node178", "@target": "node179"}, "edge175": {"@length": 0.000691, "@source": "node178", "@target": "node180"}}, "node180": {"edge176": {"@length": 1e-06, "@source": "node180", "@target": "node181"}, "edge177": {"@length": 0.00075, "@source": "node180", "@target": "node182"}}}, "nodeById": {"node140": {"@root": true}, "node141": {}, "node142": {}, "node143": {"@otu": "otu91"}, "node144": {}, "node145": {}, "node146": {"@otu": "otu92"}, "node147": {}, "node148": {}, "node149": {}, "node150": {"@otu": "otu93"}, "node151": {"@otu": "otu94"}, "node152": {}, "node153": {}, "node154": {}, "node155": {}, "node156": {"@otu": "otu95"}, "node157": {"@otu": "otu96"}, "node158": {"@otu": "otu97"}, "node159": {"@otu": "otu98"}, "node160": {"@otu": "otu99"}, "node161": {}, "node162": {}, "node163": {"@otu": "otu100"}, "node164": {}, "node165": {"@otu": "otu101"}, "node166": {"@otu": "otu102"}, "node167": {"@otu": "otu103"}, "node168": {"@otu": "otu104"}, "node169": {}, "node170": {"@otu": "otu105"}, "node171": {}, "node172": {"@otu": "otu106"}, "node173": {}, "node174": {"@otu": "otu107"}, "node175": {"@otu": "otu108"}, "node176": {}, "node177": {"@otu": "otu109"}, "node178": {}, "node179": {"@otu": "otu110"}, "node180": {}, "node181": {"@otu": "otu111"}, "node182": {"@otu": "otu112"}}}}}}}}, "branch2sha": {"master": "3f065dbdd4e1ea1f2e623d3c6431b35210dcfed5"}, "commentHTML": "", "duplicateStudyIDs": [], "shardName": "phylesystem-1", "versionHistory": [{"id": "ca698285c889edf4de67c8ce184ad021f91a875a", "author_name": "Ruth Timme", "author_email": "ANONYMOUS", "date": "Wed, 21 Feb 2018 15:43:22 +0000", "date_ISO_8601": "2018-02-21 15:43:22 +0000", "relative_date": "8 years ago", "message_subject": "updated GitGub link", "message_body": "(Update document 'ot_301' via OpenTree API)"}, {"id": "f1f721e6016a36e611aab989317dc2573eb12322", "author_name": "Ruth Timme", "author_email": "ANONYMOUS", "date": "Tue, 20 Feb 2018 18:27:57 +0000", "date_ISO_8601": "2018-02-20 18:27:57 +0000", "relative_date": "8 years ago", "message_subject": "Update document 'ot_301' via OpenTree API"}, {"id": "bcfcefb7f7d427c8c825e86abca4ee5aed9a8be1", "author_name": "Ruth Timme", "author_email": "ANONYMOUS", "date": "Tue, 20 Feb 2018 18:26:24 +0000", "date_ISO_8601": "2018-02-20 18:26:24 +0000", "relative_date": "8 years ago", "message_subject": "Update document 'ot_301' via OpenTree API"}, {"id": "cf89e9f6c081bf99d0decf0e1c069baeef74d30e", "author_name": "Ruth Timme", "author_email": "ANONYMOUS", "date": "Wed, 23 Aug 2017 19:58:30 +0000", "date_ISO_8601": "2017-08-23 19:58:30 +0000", "relative_date": "9 years ago", "message_subject": "added campy tree", "message_body": "(Update document 'ot_301' via OpenTree API)"}, {"id": "7431fbf978e8ae93d6a9ab3e495f281aaa1e9979", "author_name": "Ruth Timme", "author_email": "ANONYMOUS", "date": "Wed, 6 Jul 2016 17:45:00 +0000", "date_ISO_8601": "2016-07-06 17:45:00 +0000", "relative_date": "10 years ago", "message_subject": "Update document 'ot_301' via OpenTree API"}, {"id": "7c7a67a0e266dd61f4e94071010aa4603fd73ad9", "author_name": "Ruth Timme", "author_email": "ANONYMOUS", "date": "Wed, 6 Jul 2016 17:41:15 +0000", "date_ISO_8601": "2016-07-06 17:41:15 +0000", "relative_date": "10 years ago", "message_subject": "Update document 'ot_301' via OpenTree API"}, {"id": "ace59a2f5fa831419627a94fa1ac0384b75c3d01", "author_name": "Ruth Timme", "author_email": "ANONYMOUS", "date": "Tue, 5 Jul 2016 21:06:35 +0000", "date_ISO_8601": "2016-07-05 21:06:35 +0000", "relative_date": "10 years ago", "message_subject": "Update document 'ot_301' via OpenTree API"}, {"id": "4b379419f90f93ffab78f1c9ae6454b0ded17f76", "author_name": "Ruth Timme", "author_email": "ANONYMOUS", "date": "Thu, 24 Sep 2015 13:48:55 +0000", "date_ISO_8601": "2015-09-24 13:48:55 +0000", "relative_date": "11 years ago", "message_subject": "Update Study #ot_301 via OpenTree API"}, {"id": "ef6a1f6bdfbb4299483f2ac25eb070f1356a9136", "author_name": "Ruth Timme", "author_email": "ANONYMOUS", "date": "Mon, 20 Jul 2015 13:52:58 +0000", "date_ISO_8601": "2015-07-20 13:52:58 +0000", "relative_date": "11 years ago", "message_subject": "Update Study #ot_301 via OpenTree API"}, {"id": "3e19be481a6bda20fdb9c6ace740ac5d177e9f99", "author_name": "Ruth Timme", "author_email": "ANONYMOUS", "date": "Mon, 20 Jul 2015 13:51:20 +0000", "date_ISO_8601": "2015-07-20 13:51:20 +0000", "relative_date": "11 years ago", "message_subject": "Update Study #ot_301 via OpenTree API"}, {"id": "6268aacdce32f18013dac83fd1196a93bda8e30b", "author_name": "Ruth Timme", "author_email": "ANONYMOUS", "date": "Mon, 20 Jul 2015 13:43:51 +0000", "date_ISO_8601": "2015-07-20 13:43:51 +0000", "relative_date": "11 years ago", "message_subject": "Update Study #ot_301 via OpenTree API"}, {"id": "99cc2cb842dd638a046f9d5623fdcf417c2bccdc", "author_name": "Ruth Timme", "author_email": "ANONYMOUS", "date": "Thu, 9 Jul 2015 16:53:09 +0000", "date_ISO_8601": "2015-07-09 16:53:09 +0000", "relative_date": "11 years ago", "message_subject": "Update Study #ot_301 via OpenTree API"}, {"id": "8afc3b6e0493df0aa92d7e9da4b3d1925d572d66", "author_name": "Ruth Timme", "author_email": "ANONYMOUS", "date": "Wed, 8 Jul 2015 20:52:32 +0000", "date_ISO_8601": "2015-07-08 20:52:32 +0000", "relative_date": "11 years ago", "message_subject": "new study", "message_body": "(Update Study #ot_301 via OpenTree API)"}, {"id": "a216fead7a28fc34b1cf244ada3147cd1f0823b8", "author_name": "Ruth Timme", "author_email": "ANONYMOUS", "date": "Wed, 8 Jul 2015 20:48:41 +0000", "date_ISO_8601": "2015-07-08 20:48:41 +0000", "relative_date": "11 years ago", "message_subject": "Update Study #ot_301 via OpenTree API"}, {"id": "a9e1b7b0026defa252dc055d64632c34a07374b5", "author_name": "Ruth Timme", "author_email": "ANONYMOUS", "date": "Wed, 8 Jul 2015 20:47:23 +0000", "date_ISO_8601": "2015-07-08 20:47:23 +0000", "relative_date": "11 years ago", "message_subject": "Update Study #ot_301 via OpenTree API"}]}