@Manual{CRAN,
    title = {R: A Language and Environment for Statistical Computing},
    author = {{R Core Team}},
    organization = {R Foundation for Statistical Computing},
    address = {Vienna, Austria},
    year = {2015},
    url = {http://www.R-project.org/},
}

@Manual{Matrix,
    title = {Matrix: Sparse and Dense Matrix Classes and Methods},
    author = {Douglas Bates and Martin Maechler},
    year = {2015},
    note = {R package version 1.2-0},
    url = {http://CRAN.R-project.org/package=Matrix},
}

@Manual{seqLogo,
    title = {seqLogo: Sequence logos for DNA sequence alignments},
    author = {Oliver Bembom},
    note = {R package version 1.34.0},
    year = {2015} 
}

@Manual{apex,
    title = {apex: Phylogenetic Methods for Multiple Gene Data},
    author = {Thibaut Jombart and Zhian Namir Kamvar and Klaus Schliep and Rebecca Harris},
    note = {R package version 1.0.1},
    year = {2015} 
}

@Manual{Turlach2013,
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    author = {Berwin A. Turlach and Andreas Weingessel},
    year = {2013},
    note = {R package version 1.5-5},
    url = {http://CRAN.R-project.org/package=quadprog},
}


@Manual{rgl,
    title = {rgl: 3D Visualization Using OpenGL},
    author = {Daniel Adler and Duncan Murdoch and {others}},
    year = {2015},
    note = {R package version 0.95.1247},
    url = {http://CRAN.R-project.org/package=rgl},
}


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}

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@Article{Revell2014,
    Title                    = {Rphylip: an {R} interface for {PHYLIP}},
    Author                   = {Revell, Liam J. and Chamberlain, Scott A.},
    Journal                  = {Methods in Ecology and Evolution},
    Year                     = {2014},
    Number                   = {9},
    Pages                    = {976--981},
    Volume                   = {5},
    Doi                      = {10.1111/2041-210X.12233},
    ISSN                     = {2041-210X},
    Keywords                 = {phylogeny, statistics, computational biology, evolution},
    Url                      = {http://dx.doi.org/10.1111/2041-210X.12233}
}

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}

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}


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  }

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}


@Book{ Paradis2012,
	Author = "Emmanuel Paradis",
	Title = "Analysis of Phylogenetics and Evolution with R",
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}


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	author = "D. Charif and J.R. Lobry",
	title = "Seqin{R} 1.0-2: a contributed package to the {R} project for statistical computing devoted to biological sequences retrieval and analysis.",
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	year = "2007",
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	address = "New York",
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	note = "{ISBN :} 978-3-540-35305-8"
}

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	title = "phangorn: Phylogenetic analysis in {R}",
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    eprint = {http://bioinformatics.oxfordjournals.org/content/27/4/592.full.pdf+html}, 
}


@Thesis{Schliep2009,
    author = "Klaus Schliep",
    title = "Some Applications of statistical phylogenetics",
    year = 2009
}


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}

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	number = "4",
	pages = "1393--1405"
}

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@Article{ Lapointe2010,
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}

@article{Wilkinson2007,
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}

@article{Warnow2012,
    title = "Standard maximum likelihood analyses of alignments with gaps can be statistically inconsistent",
    journal = "PLOS Currents Tree of Life",
    year = "2012",
    doi = "10.1371/currents.RRN1308",
    author = "Tandy Warnow"  
}

