python外文文献.docx

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python外文文献

apythonEnvironmentforTreeExploration

ReviewedbyJaimeHuerta-Cepas,correspondingauthorlJoaqunDopazo,2and

ToniGabald6ncorrespondingauthor1

Abstract

Manybioinformaticsanalyses,rangingfromgeneclusteringtophylogenetics,

producehierarchical

treesastheirmain

result.

Theseareused

torepresent

the

relationships

among

different

biological

entities,

thus

facilitating

theiranalysis

and

interpretation.

Anumberof

standalone

programs

are

available

thatfocuson

tree

visualizationorthatperformspecificanalysesonthem.However,suchapplicationsarerarelysuitableforlarge-scalesurveys,inwhichahigherlevelofautomationisrequired.Currently,manygenome-wideanalysesrelyontree-likedatarepresentationandhencethereisagrowingneedforscalabletoolstohandletreestructuresatlargescale.

Keywords:

Python,spikingneurons,simulation,integrateandfire,teaching,neuralnetworks,computationalneuroscienee,software

Background

HerewepresenttheEnvironmentforTreeExploration（ETE）,apythonprogramming

toolkitthatassistsintheautomatedmanipulation,analysisandvisualizationof

hierarchicaltrees.ETElibrariesprovideabroadsetoftreehandlingoptionsaswellasspecificmethodstoanalyzephylogeneticandclusteringtrees.Amongotherfeatures,

ETEallowsfortheindependentanalysisoftreepartitions,hassupportfortheextendednewickformat,providesanintegratednodeannotationsystemandpermitstolinktreestoexternaldatasuchasmultiplesequeneealignmentsornumericalarrays.Inaddition,ETEimplementsanumberofbuilt-inanalyticaltools,includingphylogeny-based

orthologypredictionandclustervalidationtechniques.Finally,ETE'sprogrammabletreedrawingenginecanbeusedtoautomatethegraphicalrenderingoftreeswithcustomizednode-specificvisualizations.

Conclusions

ETEprovidesacompletesetofmethodstomanipulatetreedatastructuresthatextendscurrentfunctionalityinotherbioinformatictoolkitsofamoregeneralpurpose.ETEisfreesoftwareandcanbedownloadedfromhttp:

//ete.cgenomics.org.

Treesarecommonlyusedtorepresenttheresultsofmanybioinformaticsanalyses.

Inparticular,suchtypeofbinarygraphsareidealtodescribethehierarchicalrelationshipsamongavarietyofbiologicalentities.Somecommonexamplesaretheevolutionaryanalysisofmolecularsequencesortheclusterizationofgenesandproteinsaccordingtotheirproperties.Besidestheinformationencodedinthetopologyoftrees,branchlengthscanalsobescaledtoprovideinformationonthedistancesbetweenthedifferentpartitions.Inphylogenetics,forinstanee,treesareusedtoillustratethe

evolutionaryrelationshipsamongspeciesormolecularsequences,consideringterminal

nodesasextantOperationalTaxonomicUnits（OTU）andinternalnodesastheircorrespondingancestors.Insuchphylogenetictrees,branchlengthsareusuallyproportionaltotheevolutionarydistaneeamongsequences.Otherapplications,suchastheanalysisofgeneexpression,usehierarchicalclusteringanalysistogroupgenesorexperimentalconditionsaccordingtothesimilarityoftheirexpressionpatterns.Likewise,treesareusedbymanyproteinclassificationmethodsandfortheanalysisofphylogeneticprofiles.Thus,theanalysisoftreedatastructuresisacommontaskinmanyareasofbioinformaticsandthereisaneedforanalyticalandvisualizationtools.Inthisrespect,anumberofbioinformaticprogramsdoexistthatassistintheexplorationofhierarchicaltrees.Mostofthem,however,consistofstandaloneapplicationsthatarefocusedonvisualizationand,occasionally,onperformingspecifictests.SomewellknownexamplesareTreeView[1],awidelyusedprogramforinspectingphylogenetictrees;ClusterTreeview[2],anapplicationforvisualizingmicroarrayclusteringresults;ATV

[3],ajavaprogramusedtoexplorephylogenieswhichprovidesalsosomeediting

options;MEGA[4],anevolutionarygeneticsanalysissuitethatincludesabuilt-intreeviewer;andmanyotherrecentapplications[5-8].Whilealltheseprogramsareveryusefultomanagesingletrees,theycanhardlybeautomatizedoradaptedtospecificneeds.Thus,whentheanalysisofhundredsorthousandsoftreesisrequired,theuseofstandaloneprogramsbecomesrestrictive,becauseamuchhigherlevelofautomationisrequired.Insuchcases,programmingtoolkitsrepresentamoreadequateframework,sincetheyprovidetoolsandmethodstohandledataatalowerlevel.Usingtoolkits,bioinformaticianscaneasilycreatetheirownanalysispipelinesandprogramcustomtasksoverlargecollectionsofdata[9].SeveralgenericbioinformatictoolkitsdoexistthatcoverawiderangeofprogrammingIanguagesandscopes,withBioPerl[10]and

BioPython[11]beingthemostextensivelydeveloped.Togetherwithabroadrangeof

otherfeatures,thesetoolkitsallowcertainlevelofinteractionwithtreedatastructures.

However,onlybasicactionsarecurrentlysupported.Alternatively,thePyCogent[12]and

P4http:

//bmnh.org/~pf/p4.htmlpythontoolkitscanbeusedtoextendthisfunctionality,althoughtheyaremostlyfocusedonphylogeneticreconstruction.R[13],ageneralpurposestatisticalframework,doesincludeseveralpackagestoperformstatisticaltestsonclusteringandphylogenetictrees.Nevertheless,thesepackagesarefocusedonperformingspecificanalysesratherthaninprovidingtreehandlingandmanipulationfeatures.Finally,incontrasttothegreatnumberofstandalonetreeviewers,programmingtoolkitsofferfew,ifany,graphicalrenderingpossibilities.AnintermediatealternativebetweenstandaloneviewersandprogrammatictreerenderingisthatoftheTreeDynprogram[14],whichhassupportforsomescriptingoptionsandcanbeusedtocreatefullyannotatedtreeimages.

Inresponsetotheselimitations,wepresentheretheEnvironmentforTree

Exploration（ETE）,apythonprogrammingtoolkittoanalyze,manipulateorvisualizeanykindofhierarchicaltree.Itextendsthefunctionalityinothertoolkitsandallowsahighlevelofcustomization.ETE'sdrawingfeatures,althoughlessexhaustivethanin

standaloneeditors,relyonthePythonscriptingIanguage,whichmakespossibleto

combineadvaneedtreeanalysesandtreevisualizationintoasingleprogram.Thetoolkitincludesmethodstobrowseandmanipulatetreetopologies,providessupportfortheNewHampshireeXtended（NHX）formatandallowsadvaneedactionssuchasnode

annotation,automaticrooting,cut&pastepartitions,treeconcatenation,nodesearch,

andbranchdistaneerelatedoperations.Inaddition,ETEimplementstwospecific

modulestoworkwithphylogeneticandclusteringtrees.Thephylogeneticextensionallowstreestobelinkedtotheircorrespondingmultiplesequeneealignments,includestwoorthologyandparalogypredictionalgorithms,implementstheduplicationdatingmethoddescribedin[15]andprovidesaccesstothePhylomeDBdatabase[16].Similarly,clusteringtreescanbelinkedtotheirsourcedata,whichallowstreepartitionstobeanalyzedthroughseveralvalidationtechniques.Additionally,ETEimplementsafully

programmabledrawingenginethatcanbeusedtogenerate,dynamically,customtreerepresentationsinPDForPNGformats.Thisdrawingengineisfullyintegratedwiththebuilt-inextensions,thusprovidingpre-definedvisualizationlayoutsforclusteringtreesandphylogenies.AGraphicalUserInterfaceisalsoincludedwhichallowsontheflyinteractionwithtrees.

Currently,theETEtoolkitisusedindiverseprojects,includingGEPAS[17],Phylemon[18]andPhylomeDB[15].ETEpackageanddocumentationcanbeaccessedat

http:

//ete.cgenomics.org

Implementation

ETEisentirelywritteninPython[19],aprogrammingIanguagethatoffersastrongsupportforintegrationwithotherIanguagesandtools,andwhosepopularityisraisingamongthebioinformaticscommunity[20].ETE'sphilosophyistofacilitatethe

integrationwithothertoolkitsaswellastoprovideascalableprogramarchitecture.Thus,ETEtreeobjectscanbeeasilyimportedandexpandedbyincorporatingcustommethodsandproperties.ThefunctionalityoftheETEtoolkitisdividedintoseveralpythonmodules,whichcanbeimportedatconvenience.AsummaryoffeaturesofthedifferentmodulesisshowninTable

Treehandlingmodule

ETE'smainmoduleallowstoreadandrendertreesusingthetwomostcommon

formats:

NewHampshire（NH）andNewHampshireeXtended（NHX）.Moreover,itallows

togeneraterandomtreesorcreatecustomtreestructuresfromscratch.Inorderto

increasecompatibilitywithothertools,severalnewickformatstandardsarecurrently

supportedbyETE,bothforreadingandwritingtrees（seeETE'sextended

documentation）.ETE'streesareinternallyencodedasaseriesoftreenodeinstancesconnectedfollowingaparent-childrelationship.Eachnodeisencodedasan

independentPythonobject,whichprovidesmanymethodstomanipulateits

connections（i.e.add,remove,deleteordetachnodes）andtoeasilybrowseitstopology

（i.e.treetraversalandgetterminal,children,sisterordescendantnodes）.Asa

consequenee,eachinternalnodeistreatedasafullyfeaturedsubtree,thusallowingto

analyzedifferentpartsoftreesseparately.ETE'streeobjectimplementationsupportsmultifurcationsandcanbeusedtodealwithvery