MUSCLE 5: Next-generation MUSCLE

Muscle v5 is a major re-write of MUSCLE based on new algorithms.

* 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.

* Alignment ensembles:
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.

* Manual:
https://drive5.com/muscle5/manual/

* Reference (included in the package)
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
