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wiki of malacology

MAFFT

在将序列放入系统发育的计算软件(e.g.MrBayes, RAxML等)前,应当先对序列进行一定的处理,具体流程是先进行比对(MAFFT),再进行保守区的选择(GBlocks),之后饱和度检验(DAMBE,Tracer),再是最适模型的选择(jModelTest)。

MAFFT的使用

下载地址 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                                                                                                                                                                                               
---------------------------------------------------------------------                                                                                                                                                                              
MAFFT v7.450 (2019/Aug/23)                                                                                                                                                                                                                           
MBE 30:772-780 (2013), NAR 30:3059-3066 (2002)                                                                          
https://mafft.cbrc.jp/alignment/software/                                                                       
---------------------------------------------------------------------                                                                                                                                                                                                                                                                                                   
Input file? (FASTA format; Folder="C:\mafft-7.450-win64-signed\mafft-win")                                              
@    

@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

Last updated on 1 Dec 2020
Published on 1 Dec 2020

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