MAFFT

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imported>Malacology2022年5月25日 (三) 10:51的版本 (init)
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下载地址

界面

将序列放入MAFFT.bat相同的文件夹中,双击MAFFT.bat

Active code page: 65001
    
Preparing environment to run MAFFT on Windows.
This may take a while, if real-time scanning by anti-virus software is on.                                                                                                                           
It may take a while before the calculation starts                                                                       
if being scanned by anti-virus software.                                                                                
Also consider using a faster version for Windows 10:                                                                    
https://mafft.cbrc.jp/alignment/software/wsl.html                                                                                                                                                                                               
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MAFFT v7.450 (2019/Aug/23)                                                                                                                                                                                                                           
MBE 30:772-780 (2013), NAR 30:3059-3066 (2002)                                                                          
https://mafft.cbrc.jp/alignment/software/                                                                       
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Input file? (FASTA format; Folder="C:\mafft-7.450-win64-signed\mafft-win")                                              
@    

参数

@后输入文件名称,如example.fas

Output file?
@ 

@后输入输出名称,一般喜欢加个out,此处键入exampleout.fas

Output format?
 1. Clustal format / Sorted
 2. Clustal format / Input order
 3. Fasta format   / Sorted
 4. Fasta format   / Input order
 5. Phylip format  / Sorted
 6. Phylip format  / Input order
@

选择4

Strategy?
 1. --auto
 2. FFT-NS-1 (fast)
 3. FFT-NS-2 (default)
 4. G-INS-i  (accurate)
 5. L-INS-i  (accurate)
 6. E-INS-i  (accurate)
@

选择1

Additional arguments? (--ep ## --op ## --kappa ## etc)
@      

直接Enter

command=

"/usr/bin/mafft" --auto --inputorder "16S.fas" > "16Sout.fas" OK?

@ [Y]

继续Enter,等待结果,到根目录找到example.fas即可