MEGA-CC官网 help

1. MEGA-CC is the compute core that is used by MEGA and is installed as a command-line application. This version is useful for iterative and batch analysis of multiple input data files. In order to use MEGA-CC, you first must generate a MEGA Analysis Options (.mao) file which specifies the analysis and settings to run. Then from a command shell, you execute the megacc command, passing parameters for the .mao and input data file(s). See an example here.

# Running in Command-Line Mode

MEGA is distributed with two user interfaces: a full graphical user interface (GUI) and a command-line interface ([MEGA-CC](https://www.megasoftware.net/web_help_10/MEGA-CC.htm)). The command-line interface requires a special input file called a [MEGA Analysis Options](https://www.megasoftware.net/web_help_10/MEGA_Analysis_Options_File.htm)(.mao) file which specifies the analysis to run as well as the analysis options to use. This .mao file can only be created by using the GUI interface. This example will show how to generate a .mao file with the graphical interface and then use that file to analyze a data set with MEGA-CC.

Generating the MEGA Analysis Options File

On the main MEGA window, click the Prototype button, which is near the bottom right corner of the window, to switch MEGA to the prototyping mode. A dialog will be shown that prompts for the data type to be used. In this

dialog, select Nucleotide and click OK.

Select Phylogeny | Construct/Test Neighbor-Joining Tree from the main MEGA windows launch bar.

The Analysis Preferences window will be shown. We will use the default options so in this dialog, just click the Save Settings button.

When prompted to save the .mao file, navigate to your Documents\MEGA X\Examples folder and save the file as infer_NJ_nucleotide.mao.

Close MEGA X.

Launching MEGA-CC from a command shell

Open a command shell and use the cd command to change to your Documents\MEGA X\Examples directory.

In the command shell, execute the following command:

megacc -a infer_NJ_nucleotide.mao -d Drosophila_Adh.meg -o demo

MEGA-CC will run the Phylogeny | Construct/Test Neighbor-Joining Tree analysis using the Drosophila_Adh.meg sequence alignment (located in the Examples directory) and output two files - a newick file (demo.nwk) with the newly created phylogeny and a text file (demo_summary.txt) that contains a summary of the analysis. The same steps are also used to execute any of the other analyses that are available in megacc. To see

the options that are available when using megacc, enter the following command in a command shell:

megacc -h

MEGA version 10.1.7
For 64-bit Linux
Build 10200107

Usage: megacc -a /pathTo/analysisFile.mao -d /pathTo/dataFile.meg [-t /pathTo/treeFile.nwk][OPTIONS]

   -a --analysisOptions
       MEGA Analysis Options File     *required*
       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

分析方法文件.mao的获取

蛋白序列、DNA序列以及建树基于的模型不同，具体的参数变换比较多，而linux下无法直接形成该文件，可以先借助Windows版megacc 先生成该文件。

• windows下安装MEGA-X cc

作者：草野py
链接：https://www.jianshu.com/p/7f0c8db32ef8
来源：简书
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