The first paper, published in Nucleic Acids Research, introduced the sequence alignment algorithm.
[1] This stage focuses on obtaining a more optimal tree by calculating the Kimura distance for each pair of input sequences using the multiple sequence alignment obtained in Stage one, and creates a second distance matrix.
The process of deleting an edge and aligning is repeated until convergence, or until a user-defined limit is reached.
[1] MUSCLE is often used as a replacement for Clustal, since it usually (but not always) gives better sequence alignments, depending on the chosen options.
MUSCLE is integrated into DNASTAR's Lasergene software, Geneious, and MacVector and is available in Sequencher, MEGA, and UGENE as a plug-in.
MUSCLE is also available as a web service via the European Molecular Biology Laboratory (EMBL)-European Bioinformatics Institute (EBI).