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- Katoh, Frith 2012 (Bioinformatics Advance Access)
Adding unaligned sequences into an existing alignment using MAFFT
and LAST.
(describes the --add and --addfragments options)
- Katoh, Toh 2010 (Bioinformatics 26:1899-1900)
Parallelization of the MAFFT multiple sequence alignment program.
(describes the multithread version)
- Katoh, Asimenos, Toh 2009 (Methods in Molecular Biology 537:39-64)
Multiple Alignment of DNA Sequences with MAFFT. In Bioinformatics
for DNA Sequence Analysis edited by D. Posada
(outlines DNA alignment methods and several tips including
group-to-group alignment and rough clustering of a large
number of sequences)
- Katoh, Toh 2008 (BMC Bioinformatics 9:212)
Improved accuracy of multiple ncRNA alignment by incorporating
structural information into a MAFFT-based framework.
(describes RNA structural alignment methods)
- Katoh, Toh 2008 (Briefings in Bioinformatics 9:286-298)
Recent developments in the MAFFT multiple sequence alignment
program.
(outlines version 6; Fast Breaking Paper in Thomson Reuters'
ScienceWatch)
- Katoh, Toh 2007 (Bioinformatics 23:372-374) Errata
PartTree: an algorithm to build an approximate tree from a large
number of unaligned sequences.
(describes the PartTree algorithm)
- Katoh, Kuma, Toh, Miyata 2005 (Nucleic Acids Res. 33:511-518)
MAFFT version 5: improvement in accuracy of multiple sequence
alignment.
(describes [ancestral versions of] the G-INS-i, L-INS-i and
E-INS-i strategies)
- Katoh, Misawa, Kuma, Miyata 2002 (Nucleic Acids Res. 30:3059-3066)
MAFFT: a novel method for rapid multiple sequence alignment based
on fast Fourier transform.
(describes the FFT-NS-1, FFT-NS-2 and FFT-NS-i strategies)
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