@Article{ Rambaut1997,
	Author = "A. Rambaut and N.C. Grassly",
	Title = "Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees",
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	Pages = "235--238",
	Year = "1997"
}

@Article{ Stefankovic2007a,
	Author = "D. Stefankovic and E. Vigoda",
	Title = "Pitfalls of heterogeneous processes for phylogenetic reconstruction",
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	Number = "1",
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	Year = "2007"
}

@Article{ Nixon1999,
	Author = "K. Nixon",
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	Year = "1999"
}

@Article{ Matsen2007,
	Author = "F. A. Matsen and M. Steel",
	Title = "Phylogenetic mixtures on a single tree can mimic a tree of another topology",
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	Number = "5",
	Pages = "767--775",
	Year = "2007"
}

@Article{ Pagel2004,
	Author = "Mark Pagel and Andrew Meade",
	Title = "A Phylogenetic Mixture Model for Detecting Pattern-Heterogeneity in Gene Sequence or Character-State Data",
	Journal = "Systematic Biology",
	Volume = "53",
	Number = "4",
	Pages = "571--581",
	Abstract = "We describe a general likelihood-based mixture model for inferring phylogenetic trees from gene-sequence or other character-state data. The model accommodates cases in which different sites in the alignment evolve in qualitatively distinct ways, but does not require prior knowledge of these patterns or partitioning of the data. We call this qualitative variability in the pattern of evolution across sites pattern-heterogeneity to distinguish it from both a homogenous process of evolution and from one characterized principally by differences in rates of evolution. We present studies to show that the model correctly retrieves the signals of pattern-heterogeneity from simulated gene-sequence data, and we apply the method to protein-coding genes and to a ribosomal 12S data set. The mixture model outperforms conventional partitioning in both these data sets. We implement the mixture model such that it can simultaneously detect rate- and pattern-heterogeneity. The model simplifies to a homogeneous model or a rate-variability model as special cases, and therefore always performs at least as well as these two approaches, and often considerably improves upon them. We make the model available within a Bayesian Markov-chain Monte Carlo framework for phylogenetic inference, as an easy-to-use computer program. [Bayesian inference; MCMC; mixture model; phylogeny; rate-heterogeneity; secondary structure; sequence evolution]",
	Year = "2004"
}

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	Author = "B. Kolaczkowski and J. W. Thornton",
	Title = "Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous",
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	Pages = "980--984",
	Year = "2004"
}

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}

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	Author = "N. Saitou and M. Nei",
	Title = "The Neighbor-Joining Method - a New Method for Reconstructing Phylogenetic Trees",
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@Article{ Pagel2008,
	Author = "Mark Pagel and Andrew Meade",
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	Pages = "3955--3964",
	Year = "2008"
}

@InCollection{ Pagel2005,
	Author = "Mark Pagel and Andrew Meade",
	Title = "Mixture models in phylogenetic inference",
	BookTitle = "Mathematics of evolution and phylogeny",
	Editor = "Olivier Gascuel",
	Publisher = "Oxford",
	Address = "New York",
	Year = "2005"
}

@Article{ Kolaczkowski2008,
	Author = "Bryan Kolaczkowski and Joseph W. Thornton",
	Title = "A Mixed Branch Length Model of Heterotachy Improves Phylogenetic Accuracy",
	Journal = "Molecular Biology and Evolution",
	Volume = "25",
	Number = "6",
	Pages = "1054--1066",
	Year = "2008"
}

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@Book{ Felsenstein2004,
	Author = "Joseph Felsenstein",
	Title = "Inferring Phylogenies",
	Publisher = "Sinauer Associates",
	Address = "Sunderland",
	Year = "2004"
}

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	Author = "Joseph Felsenstein",
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@Book{ Yang2006,
	Author = "Ziheng Yang",
	Title = "Computational Molecular evolution",
	Publisher = "Oxford University Press",
	Address = "Oxford",
	Year = "2006"
}

@Article{ Paradis2004,
	Author = "E. Paradis and J. Claude and K. Strimmer",
	Title = "APE: Analyses of Phylogenetics and Evolution in R language",
	Journal = "Bioinformatics",
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	Year = "2004"
}

@Book{ Paradis2006,
	Author = "Emmanuel Paradis",
	Title = "Analysis of Phylogenetics and Evolution with R",
	Publisher = "Springer",
	Address = "New York",
	Year = "2006"
}

@InCollection{ seqinr,
	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.",
	booktitle = "Structural approaches to sequence evolution: Molecules, networks, populations",
	year = "2007",
	editor = "M. Porto H.E. Roman {U. Bastolla} and M. Vendruscolo",
	series = "Biological and Medical Physics, Biomedical Engineering",
	pages = "207--232",
	address = "New York",
	publisher = "Springer Verlag",
	note = "{ISBN :} 978-3-540-35305-8"
}

@Article{ Mathews2010,
	Author = "S. Mathews and M.D. Clements and M.A. Beilstein",
	Title = "A duplicate gene rooting of seed plants and the phylogenetic position of flowering plants.",
	Journal = "Phil. Trans. R. Soc. B",
	Volume = "365",
	Pages = "383--395",
	Year = "2010"
}

@Article{ Schliep2010,
	title = "phangorn: Phylogenetic analysis in {R}",
	author = "Klaus Peter Schliep",
	journal = "Bioinformatics",
  	year = "2011",
	volume = "27",
	number = "4",
        pages = "592--593",
}

@Article{ Schliep2010b,
	title = "Harvesting Evolutionary Signals in a Forest of Prokaryotic Gene Trees",
	author = "Klaus Schliep, Philippe Lopez, Franois-Joseph Lapointe and ric Bapteste",
	journal = "Molecular Biology and Evolution",
	year = "2010",
	note = "doi:10.1093/molbev/msq323"
}

@Article{ Swofford1987,
	title = "Reconstructing ancestral character states under Wagner parsimony",
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	journal = "Math. Biosci.",
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	Volume = "87",
	pages = "199--229"
}

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@article{Posada2008,
    author = {Posada, David}, 
    title = {jModelTest: Phylogenetic Model Averaging}, 
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    pages = {1253-1256}, 
    year = {2008}, 
    URL = {http://mbe.oxfordjournals.org/content/25/7/1253.abstract}, 
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}

@article{Hendy1982,
    author = {Hendy, M.D. and Penny D.}, 
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}



