Run MAFFT multiple sequence alignment

MAFFT (Multiple Alignment using Fast Fourier Transform) is a fast, widely used tool for aligning DNA and protein sequences so that corresponding positions can be compared. It is commonly used to prepare unaligned FASTA sequences for phylogenetic tree inference. You can let MAFFT select an appropriate algorithm automatically, choose a preset optimized for speed, accuracy, or very large datasets, and fine-tune advanced settings when needed. Phylomena records the selected settings, command, input, and aligned FASTA result for reproducibility.