Clustal Omega for making accurate alignments of many protein sequences

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Generating functional protein variants with variational autoencoders (2020, methodology): “Multiple sequence alignment To create a multiple sequence alignment from the dataset, the 375 full set of training and validation sequences were aligned using Clustal Omega [29] using the profile 376 HMM of the bacterial luciferase family from PFAM [36] as an external profile alignment to guide the ”
VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center (2021, methodology): “A gene’s sequence can be aligned with the sequences of its orthologs and paralogs using the Clustal Omega (8) alignment tool.”