Nat Commun. 2022 Nov 15;13(1):6968. doi:10.1038/s41467-022-34630-w

Edgar RC.

Muscle5: High-accuracy alignment ensembles enable unbiased assessments of sequence homology and phylogeny.

Random variations of HMM parameters and guide trees in different replicates to explore systematic biases and remove them by averaging the replicates. “Unlike typical conservation-based metrics, a column with many gaps or with biochemically dissimilar amino acids will be assigned high [confidence] if it is consistently reproduced.”