slackbuilds_ponce/academic/mafft/References

- 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)