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This article introduces you how to use mafft for multi-sequence alignment, the content is very detailed, interested friends can refer to, hope to be helpful to you.

For multiple sequence alignment of thousands of sequences, muscle is usually the best choice in terms of accuracy and running speed. But muscle's memory optimization is not good, and if you need more memory than the machine memory, you can consider mafft at this time.

Mafft is a cross-platform tool that supports the following platforms

The basic usage of the software is as follows

Mafft input > output

Input is the input sequence file in fasta format, and output is the output result file in fasta format. Mafft supports multiple sequence alignment of nucleic acid and protein sequences, and has built-in a variety of sequence alignment algorithms, which can be divided into the following three categories

Consistency based methods

Iterative refinment methods

Progressive methods

These three kinds of algorithms have their own advantages in accuracy and speed, 3 > 2 > 1 for running speed and 1 > 2 > 3 for accuracy.

1. Consistency based methods

This kind of algorithm includes L-INS-i, E-INS-i and G-INS-i.

The usage of L-INS-i is as follows

Mafft-- localpair-- maxiterate 1000 input_file > output_file

The usage of E-INS-i is as follows

Mafft-- genafpair-- maxiterate 1000 input_file > output_file

The usage of G-INS-i is as follows

Mafft-globalpair-maxiterate 1000 input_file > output_file2. Iterative refinment methods

This kind of algorithm includes two algorithms: FFT-NS-i and NW-NS-i.

The usage of FFT-NS-i is as follows

Mafft-- maxiterate 1000 input_file > output_file

The usage of NW-NS-i is as follows

Mafft-- maxiterate 1000 input_file > output_file3. Progressive methods

This kind of algorithm includes two algorithms: FFT-NS-1 and FFT-NS-2.

The usage of FFT-NS-1 is as follows

Mafft-- retree 1 input_file > output_file

The usage of FFT-NS-2 is as follows

Mafft-- retree 2 input_file > output_file

If you do not know how to choose the appropriate algorithm when comparing, you can use the following settings

Mafft-- auto input > output

The software will automatically select the appropriate algorithm according to the characteristics of the input sequence.

EBI also provides online services for mafft.

On how to use mafft for multi-sequence alignment to share here, I hope the above content can be of some help to you, can learn more knowledge. If you think the article is good, you can share it for more people to see.

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