最新python外文文献.docx
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最新python外文文献.docx
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最新python外文文献
apythonEnvironmentforTreeExploration
ReviewedbyJaimeHuerta-Cepas,correspondingauthor1JoaquínDopazo,2andToniGabaldóncorrespondingauthor1
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.ETEisfreesoftwareandcanbedownloadedfromhttp:
//ete.cgenomics.org.
Treesarecommonlyusedtorepresenttheresultsofmanybioinformaticsanalyses.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]andP4http:
//bmnh.org/~pf/p4.htmlpythontoolkitscanbeusedtoextendthisfunctionality,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].ETEpackageanddocumentationcanbeaccessedathttp:
//ete.cgenomics.org
Implementation
ETEisentirelywritteninPython[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(i.e.add,remove,deleteordetachnodes)andtoeasilybrowseitstopology(i.e.treetraversalandgetterminal,children,sisterordescendantnodes).Asaconsequence,eachinternalnodeistreatedasafullyfeaturedsubtree,thusallowingtoanalyzedifferentpartsoftreesseparately.ETE'streeobjectimplementationsupportsmultifurcationsandcanbeusedtodealwithverylargestructures.Asareference,theNCBItaxonomynewicktreefile,withmorethan450.000nodes,couldbeloadedasanETEtreeobjectin40seconds(IntelXeonCPU2.33GHz).
OneofthemainadvantagesofETEascomparedtoothertoolkitsisthatnodescancontainadditionalinformationotherthantopologyandbranchdistances.Usersarefreetoassociateanyexternaldatatothedifferenttreenodesandthenuse
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