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EXTERNAL TOOL CITATIONS: Please remember to cite the aligner and tree inference tools that you use during the course of a SATe run. The exact citation will depend on what tools you choose to use. Mafft (mafft, disttbfast, dvtditr, pairlocalalign, tbfast): See the References section on http://mafft.cbrc.jp/alignment/software/ RAxML: See the Publications section on http://wwwkramer.in.tum.de/exelixis/publications.html Opal: Wheeler, T.J. and Kececioglu, J.D. "Multiple alignment by aligning alignments," Proceedings of the 15th ISCB Conference on Intelligent Systems for Molecular Biology, Bioinformatics 23, i559-i568, 2007. And see http://opal.cs.arizona.edu/ Muscle: Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput.Nucleic Acids Res. 32(5):1792-1797. doi:10.1093/nar/gkh340 Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity BMC Bioinformatics, (5) 113. doi:10.1186/1471-2105-5-113. See http://www.drive5.com/muscle/ Clustal: See the References section of ftp://ftp.ebi.ac.uk/pub/software/clustalw2/clustalx_help.html Prank: See http://www.ebi.ac.uk/goldman-srv/prank/prank FastTree: Price MN, Dehal PS, Arkin AP. (2010) FastTree 2: Approximately Maximum-Likelihood Trees for Large Alignments. PLoS ONE 5(3): e9490. doi:10.1371/journal.pone.0009490. HMMER: See citations on [HMMER website](http://hmmer.janelia.org/).
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