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Frequently Asked Questions for SATé
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Q: What does "SATé" mean?
A: Simultaneous Alignment and Tree Estimation.

Q: How is "SATé" pronounced?
A: Sah-tay 

Q: What formats does SATé use?
A: FASTA for sequences, and Phylip for trees (if you are using RAxML, then some
    of the temporary files that are saved will be in the relaxed phylip format).

Q: Where can I find the description of SATé algorithm?
A: Please refer to:
      Liu, K., S. Raghavan, S. Nelesen, C. R. Linder, T. Warnow, "Rapid and
      Accurate Large-Scale Co-estimation of Sequence Alignments and Phylogenetic
      Trees", 2009, Science, 324, 1561-1564.
   for a description of the first variant of the algorithm.  The current 
   implementation is most similar to:
      Liu, K., T.J. Warnow, M.T. Holder, S. Nelesen, J. Yu, A. Stamatakis, and
      C.R. Linder, "SATé-II: Very Fast and Accurate Simultaneous Estimation of
      Multiple Sequence Alignments and Phylogenetic Trees." Systematic Biology.
      61(1):90-106.

Q: Which alignment programs are included with SATé distribution?
A: CLUSTALW 2.0.12
   MAFFT 6.717
   MUSCLE 3.7
   OPAL 1.0.3
   PRANK 100311

Q: Which phylogenetic tree reconstruction programs are in SATé distribution?
   RAxML 7.2.6
   FastTree 2.1.4

Q: How to cite SATé software?
A: Please cite the two algorithm papers, the software, and the appropriate
   external tools.

    ALGORITHM CITATIONS:
    Liu, K., S. Raghavan, S. Nelesen, C. R. Linder, T. Warnow, 2009. "Rapid and
        accurate large scale coestimation of sequence alignments and
        phylogenetic trees." Science, 324(5934):1561-1564, 19 June 2009,
        doi: 10.1126/science.1171243
    Liu, K., T.J. Warnow, M.T. Holder, S. Nelesen, J. Yu, A. Stamatakis, and
        C.R. Linder. "SATé-II: Very Fast and Accurate Simultaneous Estimation of
        Multiple Sequence Alignments and Phylogenetic Trees." Systematic
        Biology. 61(1):90-106

    CITATIONS FOR THE SATé SOFTWARE ITSELF AND ITS DEPENDENCIES:
    Jiaye Yu, and Mark T. Holder "SATé version VERSION_NUMBER_HERE" from
        http://phylo.bio.ku.edu/software/sate/sate.html DATE DOWNLOADED. (for
        version 1.2 or earlier)
    Jiaye Yu, Mark T. Holder, Jeet Sukumaran, and Siavash Mirarab "SATé version
        VERSION_NUMBER_HERE" from
        http://phylo.bio.ku.edu/software/sate/sate.html DATE DOWNLOADED. (for
        version 1.2.1 to 2.1.0)
    Jiaye Yu, Mark T. Holder, Jeet Sukumaran, Siavash Mirarab, and Jamie Oaks
        "SATé version VERSION_NUMBER_HERE" from
        http://phylo.bio.ku.edu/software/sate/sate.html DATE DOWNLOADED. (for
        version 2.2.0 or later)
    Sukumaran, J. and Mark T. Holder. 2010. "DendroPy: A Python library for
        phylogenetic computing". Bioinformatics 26:1569-1571. (for all SATé
        versions from this website)

    EXTERNAL TOOL CITATIONS:
    Please remember to cite the aligner and tree inference tools that you use
    during the course of a SATé run. The exact citation will depend on what
    tools you choose to use.

    Mafft: 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.

Q: What is going on if I see a message like: 
    "SATe ERROR: Error in reading the treefile, probably due to a name in the
    tree that does not match the names in the input sequence files.

    SATe ERROR: SATe is exiting because of an error:
    'Taxon "Urochroa_bougueri" not in TaxonSet, and cannot be created because
    TaxonSet is immutable' 
    "?
A: This indicates that the names of the sequences (aka 'taxa') in the tree did
    not match the names found in the FASTA file. Check the FASTA file for the
    name that appears in single quotes in the error message (this is a name 
    that was found in the tree).
