python外文文献Word文件下载.docx
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python外文文献Word文件下载.docx
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nDopazo,2andToniGabaldó
ncorrespondingauthor1
Abstract
Manybioinformaticsanalyses,rangingfromgeneclusteringtophylogenetics,producehierarchicaltreesastheirmainresult.Theseareusedtorepresenttherelationshipsamongdifferentbiologicalentities,thusfacilitatingtheiranalysisandinterpretation.Anumberofstandaloneprogramsareavailablethatfocusontreevisualizationorthatperformspecificanalysesonthem.However,suchapplicationsarerarelysuitableforlarge-scalesurveys,inwhichahigherlevelofautomationisrequired.Currently,manygenome-wideanalysesrelyontree-likedatarepresentationandhencethereisagrowingneedforscalabletoolstohandletreestructuresatlargescale.
Keywords:
Python,spikingneurons,simulation,integrateandfire,teaching,neuralnetworks,computationalneuroscience,software
Background
HerewepresenttheEnvironmentforTreeExploration(ETE),apythonprogrammingtoolkitthatassistsintheautomatedmanipulation,analysisandvisualizationofhierarchicaltrees.ETElibrariesprovideabroadsetoftreehandlingoptionsaswellasspecificmethodstoanalyzephylogeneticandclusteringtrees.Amongotherfeatures,ETEallowsfortheindependentanalysisoftreepartitions,hassupportfortheextendednewickformat,providesanintegratednodeannotationsystemandpermitstolinktreestoexternaldatasuchasmultiplesequencealignmentsornumericalarrays.Inaddition,ETEimplementsanumberofbuilt-inanalyticaltools,includingphylogeny-basedorthologypredictionandclustervalidationtechniques.Finally,ETE'
sprogrammabletreedrawingenginecanbeusedtoautomatethegraphicalrenderingoftreeswithcustomizednode-specificvisualizations.
Conclusions
ETEprovidesacompletesetofmethodstomanipulatetreedatastructuresthatextendscurrentfunctionalityinotherbioinformatictoolkitsofamoregeneralpurpose.ETEisfreesoftwareandcanbedownloadedfromarecommonlyusedtorepresenttheresultsofmanybioinformaticsanalyses.Inparticular,suchtypeofbinarygraphsareidealtodescribethehierarchicalrelationshipsamongavarietyofbiologicalentities.Somecommonexamplesaretheevolutionaryanalysisofmolecularsequencesortheclusterizationofgenesandproteinsaccordingtotheirproperties.Besidestheinformationencodedinthetopologyoftrees,branchlengthscanalsobescaledtoprovideinformationonthedistancesbetweenthedifferentpartitions.Inphylogenetics,forinstance,treesareusedtoillustratetheevolutionaryrelationshipsamongspeciesormolecularsequences,consideringterminalnodesasextantOperationalTaxonomicUnits(OTU)andinternalnodesastheircorrespondingancestors.Insuchphylogenetictrees,branchlengthsareusuallyproportionaltotheevolutionarydistanceamongsequences.Otherapplications,suchastheanalysisofgeneexpression,usehierarchicalclusteringanalysistogroupgenesorexperimentalconditionsaccordingtothesimilarityoftheirexpressionpatterns.Likewise,treesareusedbymanyproteinclassificationmethodsandfortheanalysisofphylogeneticprofiles.Thus,theanalysisoftreedatastructuresisacommontaskinmanyareasofbioinformaticsandthereisaneedforanalyticalandvisualizationtools.Inthisrespect,anumberofbioinformaticprogramsdoexistthatassistintheexplorationofhierarchicaltrees.Mostofthem,however,consistofstandaloneapplicationsthatarefocusedonvisualizationand,occasionally,onperformingspecifictests.SomewellknownexamplesareTreeView[1],awidelyusedprogramforinspectingphylogenetictrees;
ClusterTreeview[2],anapplicationforvisualizingmicroarrayclusteringresults;
ATV[3],ajavaprogramusedtoexplorephylogenieswhichprovidesalsosomeeditingoptions;
MEGA[4],anevolutionarygeneticsanalysissuitethatincludesabuilt-intreeviewer;
andmanyotherrecentapplications[5-8].Whilealltheseprogramsareveryusefultomanagesingletrees,theycanhardlybeautomatizedoradaptedtospecificneeds.Thus,whentheanalysisofhundredsorthousandsoftreesisrequired,theuseofstandaloneprogramsbecomesrestrictive,becauseamuchhigherlevelofautomationisrequired.Insuchcases,programmingtoolkitsrepresentamoreadequateframework,sincetheyprovidetoolsandmethodstohandledataatalowerlevel.Usingtoolkits,bioinformaticianscaneasilycreatetheirownanalysispipelinesandprogramcustomtasksoverlargecollectionsofdata[9].Severalgenericbioinformatictoolkitsdoexistthatcoverawiderangeofprogramminglanguagesandscopes,withBioPerl[10]andBioPython[11]beingthemostextensivelydeveloped.Togetherwithabroadrangeofotherfeatures,thesetoolkitsallowcertainlevelofinteractionwithtreedatastructures.However,onlybasicactionsarecurrentlysupported.Alternatively,thePyCogent[12]andP4~pf/pythontoolkitscanbeusedtoextendthisfunctionality,althoughtheyaremostlyfocusedonphylogeneticreconstruction.R[13],ageneralpurposestatisticalframework,doesincludeseveralpackagestoperformstatisticaltestsonclusteringandphylogenetictrees.Nevertheless,thesepackagesarefocusedonperformingspecificanalysesratherthaninprovidingtreehandlingandmanipulationfeatures.Finally,incontrasttothegreatnumberofstandalonetreeviewers,programmingtoolkitsofferfew,ifany,graphicalrenderingpossibilities.AnintermediatealternativebetweenstandaloneviewersandprogrammatictreerenderingisthatoftheTreeDynprogram[14],whichhassupportforsomescriptingoptionsandcanbeusedtocreatefullyannotatedtreeimages.
Inresponsetotheselimitations,wepresentheretheEnvironmentforTreeExploration(ETE),apythonprogrammingtoolkittoanalyze,manipulateorvisualizeanykindofhierarchicaltree.Itextendsthefunctionalityinothertoolkitsandallowsahighlevelofcustomization.ETE'
sdrawingfeatures,althoughlessexhaustivethaninstandaloneeditors,relyonthePythonscriptinglanguage,whichmakespossibletocombineadvancedtreeanalysesandtreevisualizationintoasingleprogram.Thetoolkitincludesmethodstobrowseandmanipulatetreetopologies,providessupportfortheNewHampshireeXtended(NHX)formatandallowsadvancedactionssuchasnodeannotation,automaticrooting,cut&
pastepartitions,treeconcatenation,nodesearch,andbranchdistancerelatedoperations.Inaddition,ETEimplementstwospecificmodulestoworkwithphylogeneticandclusteringtrees.Thephylogeneticextensionallowstreestobelinkedtotheircorrespondingmultiplesequencealignments,includestwoorthologyandparalogypredictionalgorithms,implementstheduplicationdatingmethoddescribedin[15]andprovidesaccesstothePhylomeDBdatabase[16].Similarly,clusteringtreescanbelinkedtotheirsourcedata,whichallowstreepartitionstobeanalyzedthroughseveralvalidationtechniques.Additionally,ETEimplementsafullyprogrammabledrawingenginethatcanbeusedtogenerate,dynamically,customtreerepresentationsinPDForPNGformats.Thisdrawingengineisfullyintegratedwiththebuilt-inextensions,thusprovidingpre-definedvisualizationlayoutsforclusteringtreesandphylogenies.AGraphicalUserInterfaceisalsoincludedwhichallowsontheflyinteractionwithtrees.
Currently,theETEtoolkitisusedindiverseprojects,includingGEPAS[17],Phylemon[18]andPhylomeDB[15].ETEpackageanddocumentationcanbeaccessedatisentirelywritteninPython[19],aprogramminglanguagethatoffersastrongsupportforintegrationwithotherlanguagesandtools,andwhosepopularityisraisingamongthebioinformaticscommunity[20].ETE'
sphilosophyistofacilitatetheintegrationwithothertoolkitsaswellastoprovideascalableprogramarchitecture.Thus,ETEtreeobjectscanbeeasilyimportedandexpandedbyincorporatingcustommethodsandproperties.ThefunctionalityoftheETEtoolkitisdividedintoseveralpythonmodules,whichcanbeimportedatconvenience.AsummaryoffeaturesofthedifferentmodulesisshowninTable
Treehandlingmodule
ETE'
smainmoduleallowstoreadandrendertreesusingthetwomostcommonformats:
NewHampshire(NH)andNewHampshireeXtended(NHX).Moreover,itallowstogeneraterandomtreesorcreatecustomtreestructuresfromscratch.Inordertoincreasecompatibilitywithothertools,severalnewickformatstandardsarecurrentlysupportedbyETE,bothforreadingandwritingtrees(seeETE'
sextendeddocumentation).ETE'
streesareinternallyencodedasaseriesoftreenodeinstancesconnectedfollowingaparent-childrelationship.EachnodeisencodedasanindependentPythonobject,whichprovidesmanymethodstomanipulateitsconnections.add,remove,deleteordetachnodes)andtoeasilybrowseitstopology.treetraversalandgetterminal,children,sisterordescendantnodes).Asaconsequence,eachinternalnodeistreatedasafullyfeaturedsubtree,thusallowingtoanalyzedifferentpartsoftreesseparately.ETE'
streeobjectimplementationsupportsmultifurcationsandcanbeusedtodealwithverylargestructures.Asareference,theNCBItaxonomynewicktreefile,withmorethannodes,couldbeloadedasanETEtreeobjectin40seconds(IntelXeonCPUGHz).
OneofthemainadvantagesofETEascomparedtoothertoolkitsisthatnodescancontainadditionalinformationotherthantopologyandbranchdistances.Usersarefreetoassociateanyexternaldatatothedifferenttreenodesandthenusesuchdatainthesubsequentanalyses,integratethemaspartoftheirtreeimagesorsavethemusingtheNHXformat.Thisfunctionalityprovidesthepossibilityofcrea
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