MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences.
MUSCLE stands for MUltiple Sequence Comparison by Log- Expectation. MUSCLE is claimed to achieve both better average accuracy and better speed than ClustalW2 or T-Coffee, depending on the chosen options.
In the authors’ tests, MUSCLE achieved the highest scores of all tested programs on several alignment accuracy benchmarks, and is also one of the fastest programs available.
Key Features
- Three different protein profile scoring functions are supported:
- log-expectation score.
- sum of pairs score using either the PAM200 matrix.
- VTML240 matrix.
- Diagonal optimization.
- Anchor optimization.
- MUSCLE uses FASTA format for both input and output formats.
- For output only, it also offers CLUSTALW, MSF, HTML, Phylip sequential and Phylip interleaved formats.
Website: www.drive5.com/muscle
Support: Documentation
Developer: Robert C. Edgar
License: Public domain
MUSCLE is written in C++. Learn C++ with our recommended free books and free tutorials.
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