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How to use muscle for multi-sequence alignment, in view of this problem, this article introduces the corresponding analysis and solution in detail, hoping to help more partners who want to solve this problem to find a more simple and feasible method.

Muscle is one of the most widely used multi-sequence alignment tools, its speed and accuracy are better than clustal, hundreds of sequences can be compared in a few seconds, and the use is simple.

On the download page, executable files for multiple operating systems are provided.

The code installed under linux is as follows

Wget https://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_i86linux64.tar.gztar xzvf muscle3.8.31_i86linux64.tar.gzmv muscle3.8.31_i86linux64 musclechmod + x muscle

Because the unzipped file name is very long, the file is renamed and executable permissions are added. For ease of calling, you can add this file to the PATH environment variable. The basic usage of muscle is as follows

Muscle-in seqs.fa-out seqs.afa

The input sequence is in FASTA format. If there is a gap in the input sequence, the gap will be removed first, and then multiple sequence alignment will be performed. The default output is also in fasta format, and other formats such as phylip, msf, clustalw and so on are also supported.

In addition to multiple sequence ratios, muscle can also build an evolutionary tree, which supports the following two ways of building trees

NJ

UPGMA

The evolutionary tree constructed by NJ method is more reliable, while the speed of UPGMA tree construction is faster. The basic usage is as follows

Muscle-maketree-in seqs.afa-out seqs.phy-cluster neighborjoining

The-cluster parameter specifies the method of building the tree. The default is upgma. The output tree file format is in Newick format.

The default parameter setting of muscle maximizes the accuracy of alignment. For large sequences, if the alignment speed is not ideal, the parameters can be adjusted appropriately.

For nucleic acid and amino acid sequences, officials recommend the fastest parameter settings, respectively.

Nucleic acid

Muscle-in seqs.fa-out seqs.afa-maxiters 1-diags

Amino acid

Muscle-in seqs.fa-out seqs.afa-maxiters 1-diags-sv-distance1 kbit20_3

When using muscle, its default parameter settings can meet most of the usage scenarios, and only for larger input sequences, the parameters need to be adjusted.

EBI provides muscle's online service at the following URL

Https://www.ebi.ac.uk/Tools/msa/muscle/

The usage is similar to that of clustal, so I won't repeat it here. For sequences with less than 500 items and the amount of data less than 1Mb, the online service can be used directly.

This is the answer to the question on how to use muscle for multi-sequence alignment. I hope the above content can be of some help to you. If you still have a lot of doubts to be solved, you can follow the industry information channel to learn more about it.

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