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