MAFFT (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "MAFFT" in English language version.

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byu.edu

scholarsarchive.byu.edu

Carroll, Hyrum; Clement, Mark; Ridge, Perry; Snell, Quinn (October 2006). "Effects of Gap Open and Gap Extension Penalties". Faculty Publications.

cbrc.jp

mafft.cbrc.jp

The base MAFFT software is distributed under one of the BSD licenses, while versions for Microsoft Windows are licensed under a GNU General Public License. Some distributions of MAFFT contain software licensed under other licenses https://mafft.cbrc.jp/alignment/software/
"MAFFT ver.7 - a multiple sequence alignment program". mafft.cbrc.jp. Retrieved 28 April 2021.
The base MAFFT software is released under one of the BSD licenses, while versions for Microsoft Windows are released under a GNU General Public License. Some distributions of MAFFT contain software licensed under other licenses https://mafft.cbrc.jp/alignment/software/

doi.org

Katoh, Kazutaka; Misawa, Kazuharu; Kuma, Kei-ichi; Miyata, Takashi (2002). "MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform". Nucleic Acids Research. 30 (14): 3059–66. doi:10.1093/nar/gkf436. PMC 135756. PMID 12136088.
Katoh, K.; Toh, H. (2006). "PartTree: An algorithm to build an approximate tree from a large number of unaligned sequences". Bioinformatics. 23 (3): 372–4. doi:10.1093/bioinformatics/btl592. PMID 17118958.
Katoh, Kazutaka; Toh, Hiroyuki (2008). "Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework". BMC Bioinformatics. 9: 212. doi:10.1186/1471-2105-9-212. PMC 2387179. PMID 18439255.
Katoh, Kazutaka; Frith, Martin C (2012). "Adding unaligned sequences into an existing alignment using MAFFT and LAST". Bioinformatics. 28 (23): 3144–6. doi:10.1093/bioinformatics/bts578. PMC 3516148. PMID 23023983.
Katoh, K.; Standley, D. M. (April 2013). "MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability". Molecular Biology and Evolution. 30 (4): 772–780. doi:10.1093/molbev/mst010. PMC 3603318. PMID 23329690.
Katoh, Kazutaka; Toh, Hiroyuki (July 2008). "Recent developments in the MAFFT multiple sequence alignment program". Briefings in Bioinformatics. 9 (4): 286–298. doi:10.1093/bib/bbn013. PMID 18372315.
Pearson, William R. (October 2013). "Selecting the Right Similarity‐Scoring Matrix". Current Protocols in Bioinformatics. 43 (1): 3.5.1–3.5.9. doi:10.1002/0471250953.bi0305s43. PMC 3848038. PMID 24509512.
Edgar, Robert; Batzoglou, Serafim (June 2006). "Multiple sequence alignment". Current Opinion in Structural Biology. 16 (3): 368–373. doi:10.1016/j.sbi.2006.04.004. PMID 16679011.
Katoh, Kazutaka (2010-04-28). "Parallelization of the MAFFT multiple sequence alignment program". Bioinformatics. 26 (15): 1899–1900. doi:10.1093/bioinformatics/btq224. PMC 2905546. PMID 20427515.
Kazunori, Yamada (4 July 2016). "Application of the MAFFT sequence alignment program to large data—reexamination of the usefulness of chained guide trees". Bioinformatics. 32 (21): 3246–3251. doi:10.1093/bioinformatics/btw412. PMC 5079479. PMID 27378296.
Kazutaka, Katoh (27 September 2012). "Adding unaligned sequences into an existing alignment using MAFFT and LAST". Bioinformatics. 28 (23): 3144–3146. doi:10.1093/bioinformatics/bts578. PMC 3516148. PMID 23023983.
Edgar, R. C. (8 March 2004). "MUSCLE: multiple sequence alignment with high accuracy and high throughput". Nucleic Acids Research. 32 (5): 1792–1797. doi:10.1093/nar/gkh340. PMC 390337. PMID 15034147.

ebi.ac.uk

"MAFFT Help and Documentation - Job Dispatcher Sequence Analysis Tools - EMBL-EBI". www.ebi.ac.uk. Retrieved 2023-04-24.

nih.gov

pubmed.ncbi.nlm.nih.gov

Katoh, Kazutaka; Misawa, Kazuharu; Kuma, Kei-ichi; Miyata, Takashi (2002). "MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform". Nucleic Acids Research. 30 (14): 3059–66. doi:10.1093/nar/gkf436. PMC 135756. PMID 12136088.
Katoh, K.; Toh, H. (2006). "PartTree: An algorithm to build an approximate tree from a large number of unaligned sequences". Bioinformatics. 23 (3): 372–4. doi:10.1093/bioinformatics/btl592. PMID 17118958.
Katoh, K.; Kuma, K.; Miyata, T.; Toh, H. (2005). "Improvement in the accuracy of multiple sequence alignment program MAFFT". Genome Informatics. International Conference on Genome Informatics. 16 (1): 22–33. PMID 16362903.
Katoh, Kazutaka; Toh, Hiroyuki (2008). "Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework". BMC Bioinformatics. 9: 212. doi:10.1186/1471-2105-9-212. PMC 2387179. PMID 18439255.
Katoh, Kazutaka; Frith, Martin C (2012). "Adding unaligned sequences into an existing alignment using MAFFT and LAST". Bioinformatics. 28 (23): 3144–6. doi:10.1093/bioinformatics/bts578. PMC 3516148. PMID 23023983.
Katoh, K.; Standley, D. M. (April 2013). "MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability". Molecular Biology and Evolution. 30 (4): 772–780. doi:10.1093/molbev/mst010. PMC 3603318. PMID 23329690.
Katoh, Kazutaka; Toh, Hiroyuki (July 2008). "Recent developments in the MAFFT multiple sequence alignment program". Briefings in Bioinformatics. 9 (4): 286–298. doi:10.1093/bib/bbn013. PMID 18372315.
Pearson, William R. (October 2013). "Selecting the Right Similarity‐Scoring Matrix". Current Protocols in Bioinformatics. 43 (1): 3.5.1–3.5.9. doi:10.1002/0471250953.bi0305s43. PMC 3848038. PMID 24509512.
Edgar, Robert; Batzoglou, Serafim (June 2006). "Multiple sequence alignment". Current Opinion in Structural Biology. 16 (3): 368–373. doi:10.1016/j.sbi.2006.04.004. PMID 16679011.
Katoh, Kazutaka (2010-04-28). "Parallelization of the MAFFT multiple sequence alignment program". Bioinformatics. 26 (15): 1899–1900. doi:10.1093/bioinformatics/btq224. PMC 2905546. PMID 20427515.
Kazunori, Yamada (4 July 2016). "Application of the MAFFT sequence alignment program to large data—reexamination of the usefulness of chained guide trees". Bioinformatics. 32 (21): 3246–3251. doi:10.1093/bioinformatics/btw412. PMC 5079479. PMID 27378296.
Kazutaka, Katoh (27 September 2012). "Adding unaligned sequences into an existing alignment using MAFFT and LAST". Bioinformatics. 28 (23): 3144–3146. doi:10.1093/bioinformatics/bts578. PMC 3516148. PMID 23023983.
Edgar, R. C. (8 March 2004). "MUSCLE: multiple sequence alignment with high accuracy and high throughput". Nucleic Acids Research. 32 (5): 1792–1797. doi:10.1093/nar/gkh340. PMC 390337. PMID 15034147.

ncbi.nlm.nih.gov

Katoh, Kazutaka; Misawa, Kazuharu; Kuma, Kei-ichi; Miyata, Takashi (2002). "MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform". Nucleic Acids Research. 30 (14): 3059–66. doi:10.1093/nar/gkf436. PMC 135756. PMID 12136088.
Katoh, Kazutaka; Toh, Hiroyuki (2008). "Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework". BMC Bioinformatics. 9: 212. doi:10.1186/1471-2105-9-212. PMC 2387179. PMID 18439255.
Katoh, Kazutaka; Frith, Martin C (2012). "Adding unaligned sequences into an existing alignment using MAFFT and LAST". Bioinformatics. 28 (23): 3144–6. doi:10.1093/bioinformatics/bts578. PMC 3516148. PMID 23023983.
Katoh, K.; Standley, D. M. (April 2013). "MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability". Molecular Biology and Evolution. 30 (4): 772–780. doi:10.1093/molbev/mst010. PMC 3603318. PMID 23329690.
Pearson, William R. (October 2013). "Selecting the Right Similarity‐Scoring Matrix". Current Protocols in Bioinformatics. 43 (1): 3.5.1–3.5.9. doi:10.1002/0471250953.bi0305s43. PMC 3848038. PMID 24509512.
Katoh, Kazutaka (2010-04-28). "Parallelization of the MAFFT multiple sequence alignment program". Bioinformatics. 26 (15): 1899–1900. doi:10.1093/bioinformatics/btq224. PMC 2905546. PMID 20427515.
Kazunori, Yamada (4 July 2016). "Application of the MAFFT sequence alignment program to large data—reexamination of the usefulness of chained guide trees". Bioinformatics. 32 (21): 3246–3251. doi:10.1093/bioinformatics/btw412. PMC 5079479. PMID 27378296.
Kazutaka, Katoh (27 September 2012). "Adding unaligned sequences into an existing alignment using MAFFT and LAST". Bioinformatics. 28 (23): 3144–3146. doi:10.1093/bioinformatics/bts578. PMC 3516148. PMID 23023983.
Edgar, R. C. (8 March 2004). "MUSCLE: multiple sequence alignment with high accuracy and high throughput". Nucleic Acids Research. 32 (5): 1792–1797. doi:10.1093/nar/gkh340. PMC 390337. PMID 15034147.

rosalind.info

"ROSALIND: Glossary: Gap penalty".

toronto.edu

cs.toronto.edu

"Windows vs. Unix Line Endings". www.cs.toronto.edu. Retrieved 2023-04-27.