MUSCLE

MUSCLE is a bioinformatics software for multiple sequence alignment of protein sequences and nucleotide sequences. It was developed by Robert C. Edgar and is available under a Nucleic Acids Research license.

Overview

MUSCLE (Multiple Sequence Comparison by Log-Expectation) is a computer program created by Robert C. Edgar for aligning multiple nucleotide or peptide sequences. MUSCLE has been cited over 6800 times, making it one of the most widely used methods in bioinformatics.

Features

MUSCLE offers a range of features that are beneficial for multiple sequence alignment. These include:

• High accuracy: MUSCLE is one of the most accurate multiple alignment programs according to published benchmark tests, with accuracy comparable to T-Coffee and MAFFT, and superior to CLUSTALW or CLUSTALX.
• Fast and scalable: MUSCLE is claimed to achieve both better average accuracy and better speed than CLUSTALW or T-Coffee, depending on the chosen options.
• Multiple sequence formats: MUSCLE can read and write several different sequence formats including FASTA, NBRF/PIR, EMBL, ClustalW, Phylip, Selex, GCG/MSF, RSF, and UCSF Chimera.

Usage

MUSCLE can be run in many modes. For a full list of options and modes, users are referred to the MUSCLE manual. The most common usage is with default parameters or using the -maxiters option for highest accuracy.

See also

• Sequence alignment
• Sequence alignment software
• List of sequence alignment software

External links

• Official website

MUSCLE Resources
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