Arlequin suite ver 3.5

种群遗传学分析软件

Molecular

EcologyResources

(2010)10,564–567doi:10.1111/j.1755-0998.2010.02847.x

COMPUTERPROGRAMNOTE

Arlequinsuitever3.5:anewseriesofprogramstoperformpopulationgeneticsanalysesunderLinuxandWindows

LAURENTEXCOFFIERandHEIDIE.L.LISCHER

CMPG,InstituteofEcologyandEvolution,UniversityofBerne,Baltzerstrasse6,3012Berne,SwitzerlandandSwissInstituteofBioinformatics,1015Lausanne,Switzerland

Abstract

WepresenthereanewversionoftheArlequinprogramavailableunderthreedifferentforms:aWindowsgraphicalversion(WINARL35),aconsoleversionofArlequin(ARLECORE),andaspeci cconsoleversiontocomputesummarystatistics(ARLSUMSTAT).Thecommand-lineversionsrununderbothLinuxandWindows.ThemaininnovationsofthenewversionincludeenhancedoutputsinXMLformat,thepossibilitytoembedgraphicsdisplayingcom-putationresultsdirectlyintooutput les,http://www.77cn.com.cnmand-lineversionsaredesignedtohandlelargeseriesof les,andARLSUMSTATcanbeusedtogeneratesummarystatisticsfromsimulateddatasetswithinanApproximateBayesianComputationframework.

Keywords:Arlequin,coalescent,graphics,populationgeneticsprogram,R,selectionReceived23December2009;revisionreceived4February2010;accepted9February2010

Progressinsequencingtechnology(e.g.Metzker2010)willsoonprovideaccesstogenome-widesequencedata-sets.Whereasthisiscurrentlyrestrictedtoafewmodelspecies,non-modelorganismswillalsosoonbene tfromthesetechnologicaladvancements(Rokas&Abbot2009),andnewtoolswillbeneededtoanalyseverylargesequencedatasetsatthepopulationlevel.Somesoftwarepackages(e.g.plinkPurcelletal.2007)havebeenspeci -callydevelopedtobothhandlesuchhugedatasetsandtodirectlyperformstatisticalanalysesonthedata.How-ever,giventherapiddevelopmentofnext-generationsequencing,itappearslikelythatspeci candspecializedsequencedatabaseswillbedeveloped(e.g.Bekeletal.2009),andstatisticalanalyseswillneedtobeperformedseparatelyonsomedatasubsets.

Whileprogramswithgraphicalinterfacesareeasiertousebymostusers,theyarenotsuitedforanalysinglargedatasets,whichismoreconvenientlycarriedoutusingcommandline-versionofsuchprograms.WedescribehereanupdatedandenhancedversionoftheARLEQUINpopulationgeneticspackage(Excof eretal.2005),includingagraphical(WINARL35)andacommand-line

(ARLECORE)versionrunningbothunderwindows,aswellascommand-line32-and64-bitLinuxARLECOREversions.ThenewversionofArlequinincludesmoreelaborateXMLoutput lesthatcanbeparsedbyRfunctionstocreateandembedgraphicaloutputsofseveralanalyses,aswellasseveralotherenhancementsdetailedlater.Finally,weprovideamodi edversionofArlequinunderWindowsandLinux,calledARLSUMSTAT,tospeci callycomputesummarystatisticsonARLEQUINinputdata les.Inadditiontotheseexecutableprograms,weprovideaseriesofbashscriptsthatcanrunnativelyunderLinux,butalsounderWindowsaftertheinstallationofaLinux-likeenvironmentlikeCYGWIN(http://www.77cn.com.cn).DetailedinformationonthenewversionofArlequin,includinganewusermanual,screenshots,accesstoallexecutable les,andscriptscanbefoundonhttp://cmpg.unibe.ch/software/arlequin35.

NoveltiesXMLoutputformat

Untilversion3.11,Arlequinproducedoutput lesinHTMLformat,andusersnowhavethepossibilitytogen-erateXML(eXtensibleMarkupLanguage)output les,whichembedstheresultsofspeci canalysesintoXML

Correspondence:LaurentExcof er,Fax:+41316314888;E-mail:Laurent.excof er@iee.unibe.ch

Ó2010BlackwellPublishingLtd

种群遗传学分析软件

tags,allowingtheirformattingbyadedicatedstylesheetandtheiranalysisbydedicatedRfunctions.

R-lequin

Wehavedevelopedspeci cRfunctionstoparseXMLoutput lesandtoproducepublication-qualitygraphicsfromtheoutputresultsdelimitedwithinXMLtags.Uponrequest,thesegraphicsarethenembeddedintotheXMLoutput lesbelowtherawresults.ThesourceoftheRfunctionsisavailableinafoldercalledRfunctioninArle-quinrootdirectory,andtheycanbecustomizedbyusersfortheirspeci cneeds.WechoseRtoproducethesegraphicsbecause(i)itisafreelyavailablepackage(http://www.77cn.com.cn/),(ii)itincludestoolsforparsingandgeneratingXML les,allowingustoaccesstagsofinteresttogettheirattributevaluesandthedatatheycontain,andformanipulatingtheXMLstructure(e.g.toaddadditionaltagsorattributes),and(iii)itpro-videsverypowerfulgraphicfacilitiesfortheproductionofmanydifferentdiagramsandplots.InclusionofPNGgraphsintoXMLoutput lesiscarriedoutbysimplypressingadedicated‘Rcmd’buttononWINARL35toolbaraftertheendofthecomputations.

Detectinglociunderselection

WehaveimplementedinArlequinver3.5aproceduretodetectlociunderselectionfromgenomescansthatcon-trastpatternsofgeneticpersitywithinandbetweenpopulations,extendingtheFDISTapproachofBeaumont&Nichols(1996)tothecasewherepopulationsarehierar-chicallystructured(seeExcof eretal.2009).Inbrief,observedlocus-speci cmeasuresofpopulationdifferen-tiation(FST)arecomparedtoanulldistributionobtainedbysimulatingsamplesunderahierarchicalislandmodel(Slatkin&Voelm1991)usingacoalescentapproach.TheP-valueofeachlocusisestimatedfromthejointdistribu-tionofheterozygosityandFSTusingakerneldensityesti-mationprocedure.Coalescentsimulationscandealwithdifferentmutationsmodels(in nite-allele,stepwisemutationmodel,oruniqueeventpolymorphisms)allow-ingonetotestmicrosatellite,standardmulti-allelic,DNAsequence,orSNPdata.AnexampleoftheoutputofagenomescananalysisdisplayingthenewgraphicsproducedbyArlequinisshowninFig.1.

Computationsatthegrouplevel

ItisnowpossibletoperformallArlequincomputationsatthegrouplevel.Ifthisoptionisselected,Arlequinwillusethegeneticstructurede nedinArlequinprojecttopoolallsamplesbelongingtoagivengroupintoasinglesampleandwillthenperformintra-andinter-population

Ó2010BlackwellPublishingLtd

COMPUTERPROGRAMNOTE565

statisticalanalysesonthesenewlyde nedsamplesandthisinadditiontothenormalanalysescarriedoutontheoriginalsamples.Notethatwiththecommand-linever-sionARLSUMSTAT,onecanchoosetocomputesummarystatisticseitheratthepopulationlevel,atthegrouplevel,oratbothlevels.Thisoptionmaybeusedtohaveanin …… 此处隐藏：10797字，全部文档内容请下载后查看。喜欢就下载吧 ……