系统发生学分析Phylip黄庆海讲义.docxVIP

文档收集于互联网，已重新整理排版 文档收集于互联网，已重新整理排版.word版本可编辑，有帮助欢迎下载支持. 1 1文档来源为:从网络收集植理Mord版本可编辑. 系统发生分析 Phylip 第一节系统发生分析简介 见教材219-221页 第二节系统发生分析算法基础 见教材221-239页 Phylip is a comprehensive phylogenetic analysis package created by Jose ph Felscnslein at the University of Washington. This package can do many of the phylogenetic analyses available in the literature today. Methods that arc available in the package include parsimony, distance matrix, and likelihood methods, including bootstrap ping and consensus trees. Data types that can be handled include molecular sequences, gene frequencies, restriction sites, distance matrices, and 0/1 (binary) discrete characters. 一.Datafile Input file The pro grams are controlled through a menu, which asks the users which options they want to set, and allows them to start the computation. The data are read into the program from a text file, which the user can prepare using any word processor or text editor (but it is important that this text file not be in the special format of that word processor ? it should instead be in flat ASCII or Text Only format). Some sequence alignment programs, like ClustalX and T-Coffee, can write data files in the PHYLIP format. Most of the programs look for the data in a file called infile. If they do not find this file they then ask the user to lypc in the file name of the data file. The file must confirm to the following: 1 ? The file begins with the information about the number of sequences and the number of nucleotides or amino acids in the alignment. The sequence names must be exactly !0 characters long - spaces arc allowed in the end. 3? Gaps must be indicated by 4, Missing data or missing information (no sequence) is indicated by ?? This is especially important in the end of the data file. Gaps (-) in the end of the data file may lead the programs to crash. 5? Spaces between the alignment blocks are allowed. This normally makes the alignment more readable. Spaces arc usually inserted into the alignment every 1