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!