Abstract
Multiple alignment of DNA sequences is an important step in various molecular biological analyses. As a large amount of sequence data is becoming available through genome and other large-scale sequencing projects, scalability, as well as accuracy, is currently required for a multiple sequence alignment (MSA) program. In this chapter, we outline the algorithms of an MSA program MAFFT and provide practical advice, focusing on several typical situations a biologist sometimes faces. For genome alignment, which is beyond the scope of MAFFT, we introduce two tools: TBA and MAUVE.
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Acknowledgments
We thank Chuong B. Do for critical reading of the manuscript.
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Katoh, K., Asimenos, G., Toh, H. (2009). Multiple Alignment of DNA Sequences with MAFFT. In: Posada, D. (eds) Bioinformatics for DNA Sequence Analysis. Methods in Molecular Biology, vol 537. Humana Press. https://doi.org/10.1007/978-1-59745-251-9_3
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DOI: https://doi.org/10.1007/978-1-59745-251-9_3
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