生物信息学实验五、多重序列比对和分子系统发育研究.doc

实验五、多重序列比对和分子系统发育分析 1、用ClustalW等软件进行序列比对 先用blastn找出多组相似序列 [2] Multiple sequence alignment [1] Confirm that all sequences are homologous [2] Adjust gap creation and extension penalties as needed to optimize the alignment [3] Restrict phylogenetic analysis to regions of the multiple sequence alignment for which data are available for all taxa (delete columns having incomplete data). [4] Many experts recommend that you delete any column of an alignment that contains gaps (even if the gap occurs in only one taxon) Figure. Evolutionary relationships of 33 taxa (linearized) The evolutionary history was inferred using the Neighbor-Joining method [1]. The optimal tree with the sum of branch length = 8is shown. The evolutionary distances were computed using the Maximum Composite Likelihood method [2] and are in the units of the number of base substitutions per site. All positions containing gaps and missing data were eliminated from the dataset (Complete deletion option). There were a total of 141 positions in the final dataset. Phylogenetic analyses were conducted in MEGA4 [3]. 1. Saitou N Nei M (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4:406-425. 2. Tamura, K., Nei, M. Kumar S. (2004) Prospects for inferring very large phylogenies by using the neighbor-joining method. PNAS 101:11030-11035. 3. Tamura K, Dudley J, Nei M Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 10.1093/molbev/msm092. Disclaimer: Although utmost care has been taken to ensure the correctness of the caption, the caption text is provided as is without any warranty of any kind. Authors advise the user to carefully check the caption prior to its use for any purpose and report any errors or problems to the authors immediately (). In no event shall the authors and their employers be liable for any damages, including but not limit