GenAlEx-6.5-Quick-Start

AbouttheSoftwareGenAlEx6.5ProudlysupportedbyTheAustralianNationalUniversity(2012)GenAlEx6.5:geneticanalysisinExcel.Populationgeneticsoftwareforteachingandresearch–anupdate.Bioinformatics28,2537-2539.PeakallR.andSmouseP.E.(2006)GenAlEx6:geneticanalysisinExcel.Populationgeneticsoftwareforteachingandresearch.Mol.Ecol.Notes6,288-295.ProfessorRodPeakallEvolution,EcologyandGeneticsResearchSchoolofBiologyTheAustralianNationalUniversity,CanberraACT0200,Australia.ProfessorPeterSmouseDepartmentofEcology,EvolutionandNaturalResourcesSchoolofEnvironmentalandBiologicalSciencesRutgersUniversity,NewBrunswickNJ08901-8551,USA.©2006to20126.5GenAlEx-GeneticAnalysisinExcel(PeakallandSmouse2006,2012)isdesignedasauser-friendlypackagewithanintuitiveandconsistentinterfacethatallowsuserstoanalyseawiderangeofpopulationgeneticdatawithinasoftwareenvironmentwithwhichmostuserswillhavesomefamiliarity(MSExcel).GenAlExisnowwidelyusedbyuniversityteachersatbothundergraduateandgraduatelevelsinAustralia,NorthAmerica,SouthAmerica,andEurope.Thesoftwarealsooffersawiderangeofanalysisoptionsforresearchers,includingsomespatialanalysisoptionsnotavailableelsewhere.Optionsforexportingdatatoawiderangeofotherpopulationgeneticpackagesarealsoprovided.Morethan6000registeredusers,representingover60countries,usethesoftware.AccordingtoISI,thefirstpaperdescribingthesoftwarewascitedmorethan2500timesintheperiod2006to2012.Peakall,R.andSmouseP.E.(2012)GenAlEx6.5:geneticanalysisinExcel.Populationgeneticsoftwareforteachingandresearch–anupdate.Bioinformatics28,2537-2539.Freelyavailableasanopenaccessarticlefrom:(2006)GENALEX6:geneticanalysisinExcel.Populationgeneticsoftwareforteachingandresearch.MolecularEcologyNotes.6,288-295.ThesoftwareandsupportingdocumentationisfreelyavailablefromTheAustralianNationalUniversity,Canberra,AustraliaatthenewURL:©PeakallandSmouse(2012)2AboutthisQuickStartDocumentThisdocumentisprovidedtoenableaquickstarttoGenAlEx6.5andneedstobereadinconjunctionwiththeReadMefiledistributedwithGenAlEx.ThisdocumentisnotintendedasasubstitutetotheTutorialsofferedwithGenAlEx,ortoreplacethecomprehensiveguidetoGenAlEx6.5andothersupportingdocumentation.SoftwareInstructionsThroughoutthistext,instructionsforusingGenAlExareprovidedinabbreviatedform.Forconsistency,thesametextstylesasusedintheGenAlEx6.5Guidehavebeenadoptedhere:Menuname(eg.GenAlEx)Menuoption(e.g.Distance)Menusuboption(e.g.Genetic)Dialogboxname(e.g.GeneticDistanceOptions)Dialogboxoption(e.g.Binary)Tipsarewritteninitalics.UnderstandingAbridgedGenAlExInstructionsFullProcedureforCalculatingGeneticDistance1.ChoosetheoptionDistancefromtheGenAlExmenu,andthenselectGeneticfromthesubmenu.2.EnsurethelocusandsampleparametersarecorrectintheGeneticDistanceOptionsdialogbox.3.SelecttheappropriateDistanceCalculation,andoutputoptionsrequired(seebelow).4.EnterTitleandWorksheetPrefixthenclickOk.Geneticdistanceisoutputtosheet[GD].AbridgedProcedureforCalculatingGeneticDistanceChooseDistance-GeneticthenselecttheappropriateDistanceCalculationintheGeneticDistanceOptionsdialogbox.NotetheabridgedoptionsomitthepromptaboutenteringaTitleandWorksheetPrefix,however,itisstronglyrecommendedthatyoutakeadvantageofthisfeaturewhichisprovidedtohelpuserskeeptrackoftheirdataanalysis.QuickStarttoGenAlEx6.5©PeakallandSmouse(2012)3GettingStartedinGenAlExBeforeyouStartBeforeyoucanworkwithGenAlExyouneedthefollowing:1.Scoredgeneticdata2.Knowledgeofwhetherthedataarebinary(haploid),binary(diploid),haploidorcodominant3.Forspatialgeneticanalysisyoualsorequiregeographicdataforindividualsandpopulations3.MicrosoftExcelinstalledonyourcomputer.InstallationGenAlExisprovidedasanExcelAdd-in,acompiledmoduleanditsassociatedGenAlExmenu.Yourdownloadedfilemayinitiallybeinthezippedformat.Usetheextractoptiontounzipthedownloadandsavethefilestoadedicatedfolderofyourchoice.YoucanworkwithGenAlExdirectlyfromthisfolder.GenAlEx6.5canberuninExcel2003onwards.GenAlEx6.5automaticallyassesseswhetherthecurrentworksheethas256columns(*.xls)or16,384columns(*.xlsx),allowingyoutoseamlesslyuseboth*.xlsand*.xlsxfilesfromwithinExcel2010,ortousethesameversionofGenAlExinbothExcel2003,orExcel2010(butnotsimultaneously,unlessusingdifferentcopies).NotesforPCusers:WestronglyrecommendthatyouuseeitherExcel2003,orExcel2010.Excel2010fixedaseriesofmajorissuesinExcel2007includingissuesthataffecttheoperationofGenAlEx.Importantly,calculationscanbeextremelyslowinExcel2007comparedwithExcel2003/2010.ItisalsoimportanttoensurethatyouhavethemostuptodatereleaseofExcel.NotesforMacintoshUsersOnMacintoshcomputers,GenAlExcanberuninExcel2004andExcel2011(releasedearlyin2010),butnotExcel2008.ThisisbecauseMicrosoftremovedtheabilityofExcel2008torunVisualBasicforApplications(VBA),themacrolanguageofMicrosoftOffice.NotethatExcel2011canonlyberunonIntel-basedMacs.BesuretoreadthereadmefileforMacusers.