pythonVersion 2.7.9 pythonImplementation CPython Bacteria false Source data for tree(s) 'tree1' tree1 Source data for tree(s) 'tree2' tree2 Source data for tree(s) 'tree3' tree3 Source data for tree(s) 'tree4' tree4 Source data for tree(s) 'tree8' tree8 ^ot:bootstrapValues ^ot:bootstrapValues ^ot:bootstrapValues ^ot:bootstrapValues ^ot:bootstrapValues ^ot:bootstrapValues ^ot:bootstrapValues ^ot:bootstrapValues ^ot:bootstrapValues ^ot:bootstrapValues ^ot:bootstrapValues ^ot:bootstrapValues ^ot:bootstrapValues ^ot:bootstrapValues ^ot:bootstrapValues ^ot:bootstrapValues ^ot:bootstrapValues ^ot:bootstrapValues ^ot:bootstrapValues ^ot:bootstrapValues ^ot:bootstrapValues ^ot:bootstrapValues ^ot:bootstrapValues ^ot:bootstrapValues ^ot:bootstrapValues ^ot:bootstrapValues ^ot:bootstrapValues ^ot:bootstrapValues ^ot:bootstrapValues ^ot:bootstrapValues ^ot:bootstrapValues ^ot:bootstrapValues ^ot:bootstrapValues ^ot:bootstrapValues ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar 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^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar otu1 otu10 otu11 otu12 otu13 otu14 otu15 otu16 otu17 otu18 otu19 otu2 otu20 otu21 otu22 otu23 otu3 otu4 otu5 otu6 otu7 otu8 otu9 otu100 otu101 otu102 otu103 otu104 otu105 otu106 otu107 otu108 otu109 otu110 otu111 otu112 otu91 otu92 otu93 otu94 otu95 otu96 otu97 otu98 otu99 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 otu55 otu56 otu58 otu59 otu57 otu60 otu61 otu62 otu63 otu65 otu66 otu67 otu68 otu69 otu70 otu71 otu72 otu73 otu74 otu75 otu76 otu77 otu78 otu79 otu80 otu81 otu82 otu83 otu84 otu85 otu86 otu87 ^ot:comment ^ot:nodeLabelMode ^ot:nodeLabelTimeUnit ^ot:reasonsToExcludeFromSynthesis ^ot:nodeLabelDescription ^ot:nodeLabelMode ^ot:nodeLabelTimeUnit ^ot:reasonsToExcludeFromSynthesis ^ot:nodeLabelDescription ^ot:nodeLabelMode ^ot:nodeLabelTimeUnit ^ot:reasonsToExcludeFromSynthesis ^ot:nodeLabelMode ^ot:nodeLabelTimeUnit ^ot:reasonsToExcludeFromSynthesis ^ot:nodeLabelMode ^ot:nodeLabelTimeUnit ^ot:reasonsToExcludeFromSynthesis tree1 tree2 tree3 tree4 Ruth Timme 844192 Bacteria (domain in cellular organisms) ot_301 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' 2017 foodborne outbreak SNP phylogeny CFSAN000211 739160 Salmonella enterica subsp. enterica serovar Bareilly CFSAN000954 739160 Salmonella enterica subsp. enterica serovar Bareilly D7328 559439 Campylobacter jejuni D7320 559439 Campylobacter jejuni D7331 559439 Campylobacter jejuni D7321 559439 Campylobacter jejuni D7329 559439 Campylobacter jejuni 2014D-0067 559439 Campylobacter jejuni 2014D-0070 559439 Campylobacter jejuni 2014D-0189 559439 Campylobacter jejuni 2014D-0068 559439 Campylobacter jejuni D5663 559439 Campylobacter jejuni CFSAN000963 739160 Salmonella enterica subsp. enterica serovar Bareilly PNUSA000195 559439 Campylobacter jejuni PNUSA000196 559439 Campylobacter jejuni PNUSA000194 559439 Campylobacter jejuni CFSAN000958 739160 Salmonella enterica subsp. enterica serovar Bareilly CFSAN000951 739160 Salmonella enterica subsp. enterica serovar Bareilly CFSAN001118 739160 Salmonella enterica subsp. enterica serovar Bareilly CFSAN000700 739160 Salmonella enterica subsp. enterica serovar Bareilly CFSAN001115 739160 Salmonella enterica subsp. enterica serovar Bareilly CFSAN000752 739160 Salmonella enterica subsp. enterica serovar Bareilly CFSAN000669 739160 Salmonella enterica subsp. enterica serovar Bareilly CFSAN000970 739160 Salmonella enterica subsp. enterica serovar Bareilly CFSAN000212 739160 Salmonella enterica subsp. enterica serovar Bareilly CFSAN001112 739160 Salmonella enterica subsp. enterica serovar Bareilly CFSAN000753 739160 Salmonella enterica subsp. enterica serovar Bareilly CFSAN000961 739160 Salmonella enterica subsp. enterica serovar Bareilly CFSAN000189 739160 Salmonella enterica subsp. enterica serovar Bareilly CFSAN002349 1038312 Listeria monocytogenes PNUSAL000957 1038312 Listeria monocytogenes MOD1 LS985 1038312 Listeria monocytogenes CFSAN023464 1038312 Listeria monocytogenes CFSAN023465 1038312 Listeria monocytogenes CFSAN023471 1038312 Listeria monocytogenes CFSAN000191 739160 Salmonella enterica subsp. enterica serovar Bareilly CFSAN023470 1038312 Listeria monocytogenes MOD1 LS997 1038312 Listeria monocytogenes MOD1 LS1011 1038312 Listeria monocytogenes MOD1 LS1003 1038312 Listeria monocytogenes MOD1 LS1009 1038312 Listeria monocytogenes MOD1 LS1006 1038312 Listeria monocytogenes MOD1 LS989 1038312 Listeria monocytogenes MOD1 LS1010 1038312 Listeria monocytogenes MOD1 LS996 1038312 Listeria monocytogenes MOD1 LS998 1038312 Listeria monocytogenes CFSAN000228 739160 Salmonella enterica subsp. enterica serovar Bareilly MOD1 LS1004 1038312 Listeria monocytogenes MOD1 LS994 1038312 Listeria monocytogenes CFSAN023468 1038312 Listeria monocytogenes MOD1 LS1008 1038312 Listeria monocytogenes CFSAN023469 1038312 Listeria monocytogenes CFSAN023463 1038312 Listeria monocytogenes MOD1 LS982 1038312 Listeria monocytogenes PNUSAL000870 1038312 Listeria monocytogenes PNUSAL001024 1038312 Listeria monocytogenes MOD1 LS995 1038312 Listeria monocytogenes CFSAN000661 739160 Salmonella enterica subsp. enterica serovar Bareilly MOD1 LS1005 1038312 Listeria monocytogenes MOD1 LS1000 1038312 Listeria monocytogenes CFSAN023466 1038312 Listeria monocytogenes CFSAN023467 1038312 Listeria monocytogenes PNUSAL000730 1038312 Listeria monocytogenes 2014C-3655 5341889 Escherichia coli 2014C-3656 5341889 Escherichia coli 2014C-3907 5251867 Escherichia coli 2011C-3609.fasta.wgsim 5341889 Escherichia coli 2014C-3857 5341889 Escherichia coli CFSAN001140 739160 Salmonella enterica subsp. enterica serovar Bareilly 2014C-3598 5251867 Escherichia coli 2014C-3600 5251867 Escherichia coli 2014C-3599 5251867 Escherichia coli 2014C-3850 5251867 Escherichia coli 2014C-3840 5251870 Escherichia coli SIM 000211 338023 Salmonella enterica (merged with Salmonella) SIM 000212 338023 Salmonella enterica (merged with Salmonella) SIM 000191 338023 Salmonella enterica (merged with Salmonella) SIM 000228 338023 Salmonella enterica (merged with Salmonella) SIM 000189 338023 Salmonella enterica (merged with Salmonella) CFSAN000968 739160 Salmonella enterica subsp. enterica serovar Bareilly SIM 000961 338023 Salmonella enterica (merged with Salmonella) SIM 000661 338023 Salmonella enterica (merged with Salmonella) SIM 001140 338023 Salmonella enterica (merged with Salmonella) SIM 000968 338023 Salmonella enterica (merged with Salmonella) SIM 000960 338023 Salmonella enterica (merged with Salmonella) SIM 000952 338023 Salmonella enterica (merged with Salmonella) SIM 000954 338023 Salmonella enterica (merged with Salmonella) SIM 000963 338023 Salmonella enterica (merged with Salmonella) SIM 000958 338023 Salmonella enterica (merged with Salmonella) SIM 000951 338023 Salmonella enterica (merged with Salmonella) CFSAN000960 739160 Salmonella enterica subsp. enterica serovar Bareilly SIM 001118 338023 Salmonella enterica (merged with Salmonella) SIM 000700 338023 Salmonella enterica (merged with Salmonella) SIM 001115 338023 Salmonella enterica (merged with Salmonella) SIM 000752 338023 Salmonella enterica (merged with Salmonella) SIM 000669 338023 Salmonella enterica (merged with Salmonella) SIM 000970 338023 Salmonella enterica (merged with Salmonella) SIM 001112 338023 Salmonella enterica (merged with Salmonella) SIM 000753 338023 Salmonella enterica (merged with Salmonella) CFSAN000952 739160 Salmonella enterica subsp. enterica serovar Bareilly D7324 559439 Campylobacter jejuni D7316 559439 Campylobacter jejuni D7333 559439 Campylobacter jejuni D7334 559439 Campylobacter jejuni D7319 559439 Campylobacter jejuni D7323 559439 Campylobacter jejuni D7327 559439 Campylobacter jejuni D7330 559439 Campylobacter jejuni D7322 559439 Campylobacter jejuni ot:undefined Myr Maximum likelihood node9 node1 false true false true false true false true false true true true false true false true false true false true false true false true false true false true false true false true false true false true false true false true false true false true false true false ot:undefined Myr Maximum likelihood node34 ot:bootstrapValues node32 false true false true false true false true false true false true false true false true false true false true false true false true false true false true false true false true false true false true false true false true false true false true false true false true false true true true false true false true false true false true false true false 100 100 100 96 43 30 67 28 79 23 4 16 36 2 1 1 58 96 45 41 49 20 100 75 46 45 71 ot:undefined Myr Maximum likelihood ot:bootstrapValues node90 false true true false true false true false true false true true true false true true true false true false 100 100 100 67 32 100 63 ot:substitutionCount Maximum likelihood node119 tree4_ROOT false true true true false true false true false true false true false true false true false true false true false true false true false true false true false true false true false true false true false true false true false true false true false true false ot:bootstrapValues Maximum likelihood node142 node140 false true true true true true true true true true true true true true true true true true true true true true true