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PHYLOViZOnline:Web-based
Phylogene8cDataAnalysisAndVisualiza8onForAllelicProfilesAndSNPData
BrunoGonçalves1,AlexandreFrancisco2,3,Cá8aVaz2,4,MárioRamirez1,JoãoCarriço1
(1)Ins8tutodeMicrobiologia,Ins8tutodeMedicinaMolecular,FaculdadedeMedicina,UniversidadedeLisboa,Lisboa,Portugal
(2)INESC-ID,R.AlvesRedol9,1000-029Lisboa,Portugal(3)Ins8tutoSuperiorTécnico,UniversidadedeLisboa,Lisboa,Portugal
(4)Ins8tutoSuperiordeEngenhariadeLisboa,Ins8tutoPolitécnicodeLisboa,007Lisboa,Portugal
AcknowledgmentsBRG was supported by grant SFRH/BD/101448/2014 from theFundaçãoparaaCiênciaeTecnologia,Portugal.
RESTfulAPI
ModifytheMinimumSpanningTree
Interac>veDistanceMatrix
UserSpecificArea
Introduc>on
ConclusionsReferences
PHYLOViZ Online is a user-friendly web applica8on, an online version of thestandalone PHYLOViZ(1), developed to allow users to perform profile baseddataanalyseswithoutsofwareinstalla8on,andtoenableaneasydataaccess,analysis, and sharing from any Internet enabled computer. It allows data setstorageandvisualiza8onthroughdis8nctvisualstrategies,andaprogramma8caccesstodatathroughaRESTfulAPIallowingittobeseamlesslyintegratedintoanythirdpartywebserviceorsofware.
PHYLOViZOnlineisfreelyavailableathEps://online.phyloviz.net
• STOREyourowndatasets.• SHAREthemthroughanuserspecificURL.• OrbymakingyourdatasetsPUBLICLYavailable.
• RETRIEVEprogramma8callypublicorregistereddata.• UPLOADdata.• RUNavailabletreealgorithmsonstoreddata.Moreinforma8onat:hEps://online.phyloviz.net/api
• Ahributecolourstonodesaccordingtoauxiliarydatafields.• LINKallnodesatagivendistance(nLVgraph)• HIDEalllinksaboveagivendistancethreshold(Treecut-off).
a) VISUALIZE pairwise distances of profiles in aheatmapdisplay.b)ORDERcellsaccordingtoauxiliarydatafields.c)EXPLOREthedistancematrixusingadynamictable.
PHYLOViZOnlineisafreelyavailableapplica8onthatprovidesaneffec8vewayforuserstovisualize,performvisual analy8csand shareannotateddata sets. It also complieswith theincreasingrequirementtomakecompletedatasetsavailableandreproducible sothattheycan be independently scru8nized. PHYLOViZ Online source code is freely available underGPLv3licenceathhps://github.com/bfrgoncalves/Online-PhyloVIZ/tree/postgres_version.AsetofNode.jsmodules isalsoavailableathhps://www.npm.com/package/phyloviz_bundlefordeveloperstoincorporatePHYLOViZtreevisualiza8onintotheirsofware.
Figure1:PHYLOViZOnlineTreevisualiza8onofadata set thatconsistsof145strains of Streptococcus pneumoniae whose par8al genome sequences arepubliclyavailable(2,3).Theprofiledataconsistsona237 locicgMLSTscheme.TheMinimum Spanning Treewas computed using the goeBURST algorithm(2)andColoursrepresentdis8nctserotypesprovidedusinganauxiliarydatafile.
Figure 3: Interac8ve Distance Matrix constructed from a node selec8on of a cgMLSTStreptococcuspneumoniaedata set.Matrix cellswereorderedaccording to serotypeandcolours representdistances computed throughpairwisecomparisonsofprofiles. Selectednodeson thedistancematrix (redborder colour)have their informa8ondisplayed in thetableaccordingtotheselectedauxiliarydatafields.
Figure 2:Different features available that modify theMinimum Spanning Tree. a) Colour assignment.Colours assigned by serotype field exis8ng in an auxiliary data file. b) n Locus Variant. All nodes withdistancesequalorabove12are linked.C)Treecut-off .All linkswitha distancevalueabove60weredeleted.
1. Francisco,A.P.,Vaz,C.,Monteiro,P.T.,Melo-Cris8no,J.,Ramirez,M.andCarriço,J.A.(2012)PHYLOViZ:phylogene>cinferenceanddatavisualiza>onfor
sequencebasedtypingmethods.BMCBioinforma3cs201516:1,13,87.2. Chewapreecha,C., Harris,S.R., Croucher,N.J., Turner,C.,Maronen,P., Cheng,L., Pessia,A., Aanensen,D.M.,Mather,A.E., Page,A.J., et al. (2014)Dense
genomicsamplingiden>fieshighwaysofpneumococcalrecombina>on.Naturegene3cs,46,305–309.3. Croucher,N.J.,Finkelstein,J.A.,Pelton,S.I.,Mitchell,P.K.,Lee,G.M.,Parkhill,J.,Bentley,S.D.,Hanage,W.P.andLipsitch,M.(2013)Popula>ongenomicsof
post-vaccinechangesinpneumococcalepidemiology.Naturegene3cs,45,656–663.4. Francisco,A.P., Bugalho,M., Ramirez,M. and Carriço,J.A. (2009)Global op>mal eBURST analysis ofmul>locus typing data using a graphicmatroid
approach.BMCBioinforma3cs201516:1,10,152.
Applica>onProgrammingInterfaceforincreasedinteroperability:
ScantoseetheVideoTutorial!