• megacc的进行多序列比对


    1.软件的安装:

    网站:http://www.megasoftware.net/

    windows上安装,下载windows-command line(cc)版本的,格式为zip,解压之后,里面有两个主程序,MEGACC和MEGA-PROTO,安装完后之后,将megacc的环境变量添加到系统的环境变量中(自行百度)

    Linux安装:根据自身系统的版本,选择相应的Linux版本,我的是Ubuntu系统,因此选择的Debian,下载最新版本

    sudo dpkg -i megaccamd64.ded ##但是Linux版本的没有mega-proto,所以还需要下载一个windows版本的megacc,借用其mega-proto生成所需要的mao文件(本人就傻的一直找Linux版本的mega-proto,发现没有,坑了一下午。。。)

    安装完成即可使用,不需要环境变量的设置。

    2.程序的运行:

    个人习惯先查看软件的使用帮助手册

    megacc -h  ##会显示megacc的具体参数意义及使用方法

    3.用法举例

    megacc   -a   setting.mao   -d    inputfile.fasta(inputfile.meg)    ##可以不指定输出选项, 

    Usage: MEGA-CC.exe -a /pathTo/analysisFile.mao -d /pathTo/dataFile.meg [-t /pathTo/treeFile.nwk][OPTIONS]
    
       -a --analysisOptions 
           MEGA Analysis Options File     *required* 由mega-proto软件产生,具体使用见下载包中附带的说明书 mao文件即参数设置文件
           Specify the full path to the Mega Analysis Options (.mao) file.  
           This file tells MEGA-CC which analysis to perform as well as
           which options to use
    
       -c --calibration 
           Calibration file *optional*
           Specify the full path to a calibration file that you wish to use. The calibration 
           file is used to provide calibration data for tree timing methods.
    
       -d --data 
           Data File         *required*
           Specify the full  or relative path to the data file you wish to 
           analyze.  MEGA (.meg), and Fasta files are supported for 
           all analyses. For distance matrices the MEGA (.meg) format is required.
    
       -f --format *applies to sequence alignment only*
           Export format for sequence alignment
           Sequence alignments can be exported in either the native .meg
           or FASTA format.
           Format values:
             MEGA
             Fasta
    
       -g --groups 
           Groups file *optional*
           Specify the full path to the groups file that you wish to use. This file organizes 
           taxa into groups where each line in the file is a key value pair of the form 
                 taxonName=groupName 
           Group information is used for certain analyses, for instance, specifying which taxon/taxa 
           comprise the outgroup for the timetree analysis 
    
       -h --help 
           Help
           Prints this help file document
       -n --noSummary: Do not write out the analysis summary file
           By default a file that gives an analysis summary is written.
           This option suppresses the export of that file. However, if
           any important messages are generated by the application, they
           will be written to this file regardless.
    
       -o --outfile     *optional*
           Output Path / Output Dir
           Specify the full path and base filename (e.g. /myResultsDirectory/myResultName) or
           simply the full path and directory of where to save the file
           (e.g. /myResultsDirectory) in which case, a unique filename will be chosen
           automatically for you.
       -pfc --partition-frequency-cutoff
           Partition Frequency Cutoff (a value between 0.0 and 1.0 - default is 0.5) *optional*
           When bootstrapping is used for tree construction a list of partitions and
           frequencies is written to a text file. The partition frequency cutoff
           causes any partitions whose frequency is less than the cutoff value
           to be ommited from this text file. Set this value to 0.0 to include
           all partitions.
       -r --recursive
           Recursive directory search *optional*
           If a directory is specified for analysis by default MEGA only searches
           the contents of that folder and not any of it's children.  To include the
           contents of all folders under the one specified, use this option.
    
       -s --silent: Do not write out the progress updates
           This option prevents progress updates from being written to stdout.
    
       -t --tree     *required for some analyses*
           Tree File
           Specify the full path to the tree file you wish to use. (Some 
           analyses requires a user provided tree, or allow you to provide 
           your own)
    
              If no output path is specified, results will be saved in the same directory
           as the input data file, with a unique name.

    不懂就看看帮助文件。。。

    4.megacc既可以分析单个的文件,也可以进行多文件处理

    单文件处理方式:

    megacc  -a  settings.mao   -d  inputfile.fasta  

    megacc   -a   settings.mao  -d   mut.txt

    在mut.txt中包含要处理的文件的路径,这样megacc就会自己按序执行(可以看出,这些待处理的文件的参数设置是一样的)

    mut.txt的内容如下所示:
    /home/lmt/Desktop/megacc/aa.meg
    /home/lmt/Desktop/megacc/bb.meg   ##记得输入绝对路径,这样可以保证不会出错

     

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  • 原文地址:https://www.cnblogs.com/lmt921108/p/8082240.html
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