A bstract Multiple Sequence Alignment (MSA) has long been a prominent and critical tool in bioinformatics and computational biology. Its importance lies in its ability to provide valuable insights into the relationships between sequences and the evolutionary pressure leading to amino acid preferences at particular sites in a protein. Despite the recent advances in protein language models, MSAs remain critical in many applications, e.g. for state-of-the-art prediction of 3D structure and protein variant effects. Se…