The MAFFT multiple sequence alignment program has been updated to Version 6, introducing two new techniques: the PartTree algorithm for improved scalability and the Four-way Consistency objective function for enhanced accuracy in aligning non-coding RNAs (ncRNAs). These updates address challenges in both scalability and accuracy of multiple sequence alignment (MSA), especially with large datasets and distantly related sequences. MAFFT now offers various options for different MSA problems, ranging from small to large alignments. Recent benchmark studies show that MAFFT is among the best choices for MSA. The PartTree algorithm allows alignment of up to 60,000 sequences with a 2% accuracy loss, while the Four-way Consistency objective function improves the accuracy of ncRNA alignments. MAFFT also supports RNA alignment with new options for structural information. The program is available online and provides alignment and phylogenetic inference services. Future directions include further improvements in RNA and protein structure alignment, scalability, and the integration of biological knowledge into MSA.The MAFFT multiple sequence alignment program has been updated to Version 6, introducing two new techniques: the PartTree algorithm for improved scalability and the Four-way Consistency objective function for enhanced accuracy in aligning non-coding RNAs (ncRNAs). These updates address challenges in both scalability and accuracy of multiple sequence alignment (MSA), especially with large datasets and distantly related sequences. MAFFT now offers various options for different MSA problems, ranging from small to large alignments. Recent benchmark studies show that MAFFT is among the best choices for MSA. The PartTree algorithm allows alignment of up to 60,000 sequences with a 2% accuracy loss, while the Four-way Consistency objective function improves the accuracy of ncRNA alignments. MAFFT also supports RNA alignment with new options for structural information. The program is available online and provides alignment and phylogenetic inference services. Future directions include further improvements in RNA and protein structure alignment, scalability, and the integration of biological knowledge into MSA.