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adding references and a few other bits to documentation for MAFFT module
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| # MAFFT Module | ||
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| This module provides a Julia wrapper for [MAFFT](http://mafft.cbrc.jp/alignment/software/). | ||
| This module provides a Julia wrapper for [MAFFT](http://mafft.cbrc.jp/alignment/software/) (Multiple alignment program for amino acid or nucleotide sequences). | ||
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| Tested with MAFFT v7.215 (2014/12/17) | ||
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| ## Usage | ||
| mafft("examples/fasta/il4.fasta") | ||
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| ## References | ||
| <ul> | ||
| <li> | ||
| Katoh, Standley 2013 | ||
| (<a href="http://mbe.oxfordjournals.org/content/30/4/772"><i>Molecular Biology and Evolution</i> <b>30</b>:772-780</a>) | ||
| <br> | ||
| MAFFT multiple sequence alignment software version 7: improvements in performance and usability. | ||
| <br> | ||
| (outlines version 7) | ||
| <li> | ||
| Kuraku, Zmasek, Nishimura, Katoh | ||
| (<a href="http://nar.oxfordjournals.org/content/41/W1/W22.abstract"><i>Nucleic Acids Research</i> <b>41</b>:W22-W28</a>) | ||
| <br> | ||
| aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity. | ||
| <br> | ||
| (describes an interactive sequence collection/selection service by <a href="http://aleaves.cdb.riken.jp/" target="_blank" onClick="_gaq.push(['_trackEvent', 'aleaves', 'link', 'server']);">aLeaves</a>, <a href="../server/">MAFFT</a> and <a href="../server/gotoaptx.html" target="_blank">Archaeopteryx</a>) | ||
| <li> | ||
| Katoh, Frith 2012 | ||
| (<a href="http://bioinformatics.oxfordjournals.org/content/28/23/3144"><i>Bioinformatics</i> <b>28</b>:3144-3146</a>) | ||
| <br> | ||
| Adding unaligned sequences into an existing alignment using MAFFT and LAST. | ||
| <br> | ||
| (describes the <a href="addsequences.html"><tt><b>--add</b></tt></a> and <a href="addsequences.html#fragments"><tt><b>--addfragments</b></tt></a> options) | ||
| <li> | ||
| Katoh, Toh 2010 | ||
| (<a href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/15/1899"><i>Bioinformatics</i> <b>26</b>:1899-1900</a>) | ||
| <br> | ||
| Parallelization of the MAFFT multiple sequence alignment program. | ||
| <br> | ||
| (describes the multithread version) | ||
| <li> | ||
| Katoh, Asimenos, Toh 2009 | ||
| (<a href="http://www.springerlink.com/content/h273273566336n74/"><i>Methods in Molecular Biology</i> <b>537</b>:39-64</a>) | ||
| <br>Multiple Alignment of DNA Sequences with MAFFT. In <i>Bioinformatics for DNA Sequence Analysis</i> edited by D. Posada | ||
| <br>(outlines DNA alignment methods and several tips including group-to-group alignment and rough clustering of a large number of sequences) | ||
| <li> | ||
| Katoh, Toh 2008 | ||
| (<a href="http://www.biomedcentral.com/1471-2105/9/212"><i>BMC Bioinformatics</i> <b>9</b>:212</a>) | ||
| <br>Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework. | ||
| <br>(describes RNA structural alignment methods) | ||
| <li> | ||
| Katoh, Toh 2008 | ||
| (<a href="http://bib.oxfordjournals.org/cgi/content/abstract/9/4/286"><i>Briefings in Bioinformatics</i> <b>9</b>:286-298</a>) | ||
| <br>Recent developments in the MAFFT multiple sequence alignment program. | ||
| <br>(outlines version 6; | ||
| <a href="http://sciencewatch.com/dr/fbp/2009/09octfbp/09octfbpKato/">Fast Breaking Paper in Thomson Reuters' ScienceWatch</a>) | ||
| <li> | ||
| Katoh, Toh 2007 | ||
| (<a href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/3/372"><i>Bioinformatics</i> <b>23</b>:372-374</a>) <a href="errata.html"><span class="redc00">Errata</span></a> | ||
| <br> | ||
| PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences. | ||
| <br> | ||
| (describes the PartTree algorithm) | ||
| <li> | ||
| Katoh, Kuma, Toh, Miyata 2005 | ||
| (<a href="http://nar.oupjournals.org/cgi/content/abstract/33/2/511"><i>Nucleic Acids Res.</i> <b>33</b>:511-518</a>) | ||
| <br> | ||
| MAFFT version 5: improvement in accuracy of multiple sequence alignment. | ||
| <br> | ||
| (describes [ancestral versions of] the G-INS-i, L-INS-i and E-INS-i strategies) | ||
| <li> | ||
| Katoh, Misawa, Kuma, Miyata 2002 | ||
| (<a href="http://nar.oupjournals.org/cgi/content/abstract/30/14/3059"><i>Nucleic Acids Res.</i> <b>30</b>:3059-3066</a>) | ||
| <br>MAFFT: a novel method for rapid multiple sequence alignment based on | ||
| fast Fourier transform. | ||
| <br> | ||
| (describes the FFT-NS-1, FFT-NS-2 and FFT-NS-i strategies) | ||
| </ul> |