MUSCLE, MUltiple Sequence Comparison by Log-Expectation, is a program for creating multiple alignments of amino acid or nucleotide sequences.  MUSCLE is claimed to achieve both better average accuracy and better speed than ClustalW2 or T-Coffee, depending on the chosen options.

To run this software interactively in a Linux environment run the commands:

module load muscle
muscle -in <seqs.fa> -out <alignedseqs.fa>

For documentation, refer to MUSCLE Homepage.

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