Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan.
Mol Biol Evol. 2013 Apr;30(4):772-80. doi: 10.1093/molbev/mst010. Epub 2013 Jan 16.
We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
我们报告了 MAFFT 多序列比对程序的一个主要更新。这个版本有几个新特性，包括在已有比对中添加未比对序列的选项、核苷酸比对方向的调整、约束比对和并行处理，这些都是在上一个主要更新后实现的。本报告展示了实际的例子来说明这些特性是如何单独和组合工作的。还展示了一些 MAFFT 错误对齐的例子，以澄清其局限性。我们讨论了如何避免错误对齐，以及我们正在努力克服这些限制。
