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