最大简约法PAUP4 系统发育树.docx

1、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File open choose NEXUS file 3. Execute 如下图：4. Analysis Heuristic search 5. Stepwise Addition random # reps:100 6. Branch Swapping Stop search after

2、 60 seconds check Save multiple trees 7. Crick OK 8. How to find the best tree from equally parsimonious trees 8.1 Trees Tree scores Likelihood 8.2. Crick Topology test (SH, KH) 8.3. Choose “Kishino-Hasegawa test” Crick OK & OK 8.4. Tree no. 1 was chosen as the best tree 9. How to save the best tree

3、 9.1. Trees Print/View trees 9.2. Choose the best tree (Example the first tree) Crick Rooting 9.3. Define Outgroup 9.4. Choose outgroup taxa OK 9.5. Save this tree as PDF 9.6. Trees Save trees to file 9.7. Trees Describe Trees Calculate CI, RI, RC values 9.8. Edit Edit Display Buffer Files Save Disp

4、lay Buffer 9.9. Close PAUP B. Bootstrap analysis1. Open PAUP Open the alignment file Execute 2. Analysis Bootstrap/Jackknife 如下图：3. Crick Continue 4. Set MaxTrees SetMax tree no. as 1000 or 100 (This depends on the size of alignment) Crick Leave unchanged, and dont prompt 如下图：5. Crick Search Wait until finishing bootstrap analysis 6. Trees Print/View Bootstrap Consensus 7. Choose outgroup taxa OK Save this tree as PDF 8. Edit Edit Display Buffer 9. Files Save Display Buffer 10. Close PAUP