Use MUSCLE v5 MSA Generation

The amino acid sequences corresponding to the proteins you want to generate an MSA for. This will not generate a seperate MSA for each provided protein but will instead generate a single MSA using all provided sequences.

The algorithm used to generate the MSA. The Muscle v5 utilizes two main algorithms for multiple sequence alignment - Parallel Perturbed Probcons (PPP) and the Super5 algorithm. PPP is a parallelized and perturbed implementation of the Probcons algorithm, enabling alignment of datasets up to a few hundred sequences. For larger datasets, Super5 applies a divide-and-conquer strategy, first identifying and removing redundant sequences, then dividing the remaining representatives into smaller clusters that can be tractably aligned by PPP. The consensus sequences from these cluster alignments are then combined using progressive alignment guided by a UPGMA tree. This hybrid approach in super5 allows Muscle v5 to effectively scale to large datasets, while maintaining high alignment accuracy compared to other state-of-the-art methods.