Linux command
mafft 命令
文本
涉及管道、覆盖或删除，执行前请先确认路径和参数。
常用示例
Align sequences (auto strategy)
mafft --auto [input.fasta] > [aligned.fasta]
Fast alignment
mafft --retree 1 [input.fasta] > [aligned.fasta]
Accurate alignment
mafft --maxiterate 1000 --localpair [input.fasta] > [aligned.fasta]
Use multiple threads
mafft --thread [8] --auto [input.fasta] > [aligned.fasta]
Add sequences to existing alignment
mafft --add [new.fasta] [existing.fasta] > [combined.fasta]
说明
MAFFT (Multiple Alignment using Fast Fourier Transform) is a high-performance multiple sequence alignment program. It offers various algorithms balancing speed and accuracy. MAFFT is widely used in bioinformatics for aligning DNA, RNA, and protein sequences.
参数
- --auto
- Auto-select strategy.
- --maxiterate _n_
- Number of iterations.
- --localpair
- Use L-INS-i (accurate).
- --globalpair
- Use G-INS-i.
- --thread _n_
- Number of threads.
- --add _file_
- Add to alignment.
- --retree _n_
- Number of tree-building iterations in progressive alignment. 1 is fast, 2 is default.
- --reorder
- Reorder output sequences by similarity.
- --adjustdirection
- Automatically detect and reverse-complement input sequences if needed.
- --quiet
- Suppress progress messages and warnings.
FAQ
What is the mafft command used for?
MAFFT (Multiple Alignment using Fast Fourier Transform) is a high-performance multiple sequence alignment program. It offers various algorithms balancing speed and accuracy. MAFFT is widely used in bioinformatics for aligning DNA, RNA, and protein sequences.
How do I run a basic mafft example?
Run `mafft --auto [input.fasta] > [aligned.fasta]` in a terminal, then adjust file names, paths, flags, or remote targets for your system.
What does --auto do in mafft?
Auto-select strategy.