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. This version supports generating an ensemble of alternative alignments with the same high accuracy obtained with default paramters. By comparing downstream predictions from different alignments, such as trees, a biologist can evaluation the robustness of conclusions against alignment errors.
Binary files are self-contained, no dependencies.
Linux muscle
Windows muscle.exe
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