A preprint of Katoh and Toh (2008, Briefings in Bioinformatics 9:286-298) Recent developments in the MAFFT multiple sequence alignment program

The accuracy and scalability of multiple sequence alignment (MSA) of DNAs and proteins have long been and are still important issues in bioinformatics. To rapidly construct a reasonable MSA, we developed the initial version of the MAFFT program in 2002. MSA software is now facing greater challenges in both scalability and accuracy than those of five years ago. As increasing amounts of sequence data are being generated by large-scale sequencing projects, scalability is now critical in many situations. The requirement of accuracy has also entered a new stage since the discovery of functional non-coding RNAs (ncRNAs); the secondary structure should be considered for constructing a high-quality alignment of distantly related ncRNAs. To deal with these prob-lems, in 2007, we updated MAFFT to version 6 with two new techniques: the PartTree algorithm and the Four-way Consistency objective function. The former improved the scalability of progres-sive alignment and the latter improved the accuracy of ncRNA alignment. We review these and other techniques MAFFT uses and suggest possible future directions of MSA software as a basis of comparative analyses. MAFFT is available a