Highest accuracy, scalable to thousands of sequences
Compared to previous versions, Muscle v5 is much more accurate, is often faster, and scales to much larger datasets. At the time of writing (late 2021), Muscle v5 has the highest scores on multiple alignment benchmarks including Balibase, Bralibase, Prefab and Balifam. It can align tens of thousands of sequences with high accuracy on a low-cost commodity computer (say, an 8-core Intel CPU with 32 Gb RAM). On large datasets, Muscle v5 is 20-30% more accurate than MAFFT and Clustal-Omega.
Muscle v5 can generate ensembles of high-accuracy alternative alignments. All replicates have equal average accuracy on benchmark test, including the MSA made with default parameters. By comparing results of downstream analysis (trees, structure prediction...) on different replicates, you can assess the effects of alignment errors on your study.