最大简约法PAUP4-系统发育树.pptxVIP

最大简约法PAUP4.0构建系统发育树

本教程将一步一步教大家怎么构建系统发育树。首先需准备用于构建系统发育树的序列fasta文件，然后将fasta序列文件使用MEGA软件进行alignment比对，再保存成nexus格式的文件用于建树。

A.?构建最大简约树（MP树）1.打开PAUP软件2.依次选择FileopenchooseNEXUSfile3.Execute

如下图：

4.AnalysisHeuristicsearch

5.StepwiseAdditionrandom#reps:100

6.BranchSwappingStopsearchafter60secondscheckSavemultipletrees

7.CrickOK

8.Howtofindthebesttreefromequallyparsimonioustrees8.1TreesTreescoresLikelihood

8.2.CrickTopologytest(SH,KH)

8.3.Choose“Kishino-Hasegawatest”CrickOKOK

8.4.Treeno.1waschosenasthebesttree

9.Howtosavethebesttree9.1.TreesPrint/Viewtrees

9.2.Choosethebesttree(Examplethefirsttree)CrickRooting

9.3.DefineOutgroup

9.4.ChooseoutgrouptaxaOK

9.5.SavethistreeasPDF9.6.TreesSavetreestofile9.7.TreesDescribeTreesCalculateCI,RI,RCvalues9.8.EditEditDisplayBufferFilesSaveDisplayBuffer9.9.ClosePAUP

B.BootstrapanalysisOpenPAUPOpenthealignmentfileExecuteAnalysisBootstrap/Jackknife

如下图：

3.CrickContinue

4.SetMaxTreesSetMaxtreeno.as1000or100(Thisdependsonthesizeofalignment)CrickLeaveunchanged,anddontprompt如下图：

5.CrickSearchWaituntilfinishingbootstrapanalysis6.TreesPrint/ViewBootstrapConsensus

7.ChooseoutgrouptaxaOKSavethistreeasPDF8.EditEditDisplayBuffer9.FilesSaveDisplayBuffer10.ClosePAUP