Multiple sequence alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and predicted structures.
MUSCLE is widely-used software for making multiple alignments of biological sequences.
Version 5 of MUSCLE achieves highest scores on Balibase, Bralibase and Balifam benchmark tests and scales to thousands of sequences on a commodity desktop computer.
This version supports generating an ensemble of alternative alignments with the same high accuracy obtained with default parameters. By comparing downstream predictions from different alignments, such as trees, a biologist can evaluation the robustness of conclusions against alignment errors.
Downloads
Binary files are self-contained, no dependencies.
https://github.com/rcedgar/muscle/releases
Documentation
Building MUSCLE from source
https://github.com/rcedgar/muscle/wiki/Building-MUSCLE
Reference
R.C. Edgar (2021) “MUSCLE v5 enables improved estimates of phylogenetic tree confidence by ensemble bootstrapping”
https://www.biorxiv.org/content/10.1101/2021.06.20.449169v1.full.pdf