BEAST软件计算分化时间.pdfVIP

RelaxedPhylogeneticsandDatingwithCondence

AlexeiJDrummondandAndrewRambaut

April1,2010

Introduction

ThispracticalwillintroducetheBEASTsoftwareforBayesianevolutionaryanalysis,

withfocusonestimatingphylogeniesanddivergencetimeswhenyouhavecalibration

informationfromfossilevidenceorotherpriorknowledge.

Youwillneedthefollowingsoftwareatyourdisposal:

BEAST-thispackagecontainstheBEASTprogram,BEAUti,TreeAnnotator

andotherutilityprograms.ThistutorialiswrittenforBEASTv1.5.x,whichhas

supportformultiplepartitions.Itisavailablefordownloadfrom

http://beast.bio.ed.ac.uk/.

Tracer-thisprogramisusedtoexploretheoutputofBEAST(andother

BayesianMCMCprograms).Itgraphicallyandquantitivelysummarizesthedis-

tributionsofcontinuousparametersandprovidesdiagnosticinformation.Atthe

timeofwriting,thecurrentversionisv1.5..Itisavailablefordownloadfrom

http://beast.bio.ed.ac.uk/.

FigTree-thisisanapplicationfordisplayingandprintingmolecularphylogenies,

inparticularthoseobtainedusingBEAST.Atthetimeofwriting,thecurrent

versionisv1.3.1.Itisavailablefordownloadfromhttp://tree.bio.ed.ac.uk/.

Ratesanddates

Thistutorialwillguideyouthroughtheanalysisofanalignmentofsequencessampled

fromtwelveprimatespecies.Thegoalistoestimatethephylogenyaswellastherate

ofevolutiononeachlineagebasedondatesofdivergenceoftheirhostspecies.

ThefirststepwillbetoconvertNEXUSfilewithDATAorCHARACTERS

blockintoBEASTXMLinputfile.ThisisdoneusingtheprogramBEAUti(this

standsforBayesianEvolutionaryAnalysisUtility).Thisisuser-friendlyprogramfor

settingtheevolutionarymodelandoptionsfortheMCMCanalysis.Thesecondstepis

toactuallyrunBEASTusingtheinputfilethatcontainsthedata,modelandsettings.

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ThefinalstepistoexploretheoutputofBEASTinorder