README.txt

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

HMMER (used for starting tree):
   Profile Hidden Markov Models. S. R. Eddy. Bioinformatics, 14:755-763, 1998.

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.