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@ARTICLE{AlfaroHolder,
	author = {Michael E. Alfaro and Mark T. Holder},
	title = {The Posterior and the Prior in {B}ayesian Phylogenetics},
	journal = {Annual Review of Ecology, Evolution, and Systematics},
	year = {2006},
	volume = {37},
	pages = {19-42},
	url = {http://arjournals.annualreviews.org/eprint/wnKYwWDmNsdHGFuWk2px/full/10.1146/annurev.ecolsys.37.091305.110021}
	}
@ARTICLE{AllmanHH2010,
	author = {Elizabeth S. Allman and Mark T. Holder and John A. Rhodes},
	title = {Estimating trees from filtered data: Identifiability of models for
	morphological phylogenetics},
	journal = {Journal of Theoretical Biology},
	year = {2010},
	volume = {263},
	pages = {108-119},
	number = {1},
	doi = {10.1016/j.jtbi.2009.12.001},
	keywords = {Mkv model},
	url = {http://www.sciencedirect.com/science/article/B6WMD-4XX160T-2/2/5adf8b8af77dd551890d7cb5b0e62dba}
	}
@ARTICLE{AyresEtAl2012,
	author = {Daniel L. Ayres and Aaron Darling and Derrick J. Zwickl and Peter
	Beerli and Mark T. Holder and Paul O. Lewis and John P. Huelsenbeck
	and Fredrik Ronquist and David L. Swofford and Michael P. Cummings
	and Andrew Rambaut and Marc A. Suchard},
	title = {{BEAGLE}: an Application Programming Interface and High-Performance
	Computing Library for Statistical Phylogenetics},
	journal = {Systematic Biology},
	year = {2012},
	volume = {61},
	pages = {170-173},
	number = {1},
	doi = {10.1093/sysbio/syr100},
	url = {http://sysbio.oxfordjournals.org/content/61/1/170.full.pdf+html}
	}
@ARTICLE{BrauerEtAl2002,
	author = {Matthew J. Brauer and Mark T. Holder and Laurie A. Dries and Derrick
	J. Zwickl and Paul O. Lewis and David M. Hillis},
	title = {Genetic Algorithms and Parallel Processing in Maximum-Likelihood
	Phylogeny Inference},
	journal = {Molecular Biology and Evolution},
	year = {2002},
	volume = {19},
	pages = {1717-1726},
	number = {10},
	url = {http://mbe.oxfordjournals.org/content/19/10/1717.full}
	}
@ARTICLE{BurnsEtAl1995a,
	author = {Burns, BM and Taylor, JF and Herring, KL and Herring, AD and Holder,
	MT and Collins, JS and Guerra, TM and Sanders, JO and Davis, SK},
	title = {Bovine microsatellite dinucleotide repeat polymorphisms at the TEXAN11,
	TEXAN12, TEXAN13, TEXAN14 and TEXAN15 loci},
	journal = {Animal Genetics},
	year = {1995},
	volume = {26},
	pages = {201--201},
	number = {3},
	doi = {10.1111/j.1365-2052.1995.tb03165.x},
	publisher = {Wiley Online Library},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2052.1995.tb03165.x/abstract}
	}
@ARTICLE{BurnsEtAl1995c,
	author = {Burns, BM and Taylor, JF and Herring, KL and Herring, AD and Holder,
	MT and Collins, JS and Guerra, TM and Sanders, JO and Davis, SK},
	title = {Bovine microsatellite mononucleotide and dinucleotide repeat polymorphisms
	at the TEXAN6, TEXAN7, TEXAN8, TEXAN9 and TEXAN10 loci},
	journal = {Animal Genetics},
	year = {1995},
	volume = {26},
	pages = {128--129},
	number = {2},
	doi = {10.1111/j.1365-2052.1995.tb02654.x},
	publisher = {Wiley Online Library},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2052.1995.tb02654.x/abstract}
	}
@ARTICLE{BurnsEtAl1995b,
	author = {Burns, BM and Taylor, JF and Herring, KL and Herring, AD and Holder,
	MT and Holder, DA and Collins, JS and Sanders, JO and Davis, SK},
	title = {Bovine microsatellite dinucleotide repeat polymorphisms at the TEXAN16,
	TEXAN17, TEXAN18, TEXAN19 and TEXAN20 loci},
	journal = {Animal Genetics},
	year = {1995},
	volume = {26},
	pages = {208--209},
	number = {3},
	doi = {10.1111/j.1365-2052.1995.tb03174.x},
	publisher = {Wiley Online Library},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2052.1995.tb03174.x/abstract}
	}
@ARTICLE{EdgcombEtAl2011,
	author = {Virginia Edgcomb and William Orsi and John Bunge and Sunok Jeon and
	Richard Christen and Chesley Leslin and Mark Holder and Gordon T.
	Taylor and Paula Suarez and Ramon Varela and Slava Epstein},
	title = {Protistan Microbial Observatory in the {Cariaco Basin, Caribbean.
	I}. Species richness and endemicity},
	journal = {ISME Journal},
	year = {2011},
	volume = {5},
	pages = {1344-1356},
	number = {8},
	doi = {10.1038/ismej.2011.6},
	url = {http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej20116a.html}
	}
@ARTICLE{EvansHBOC2010,
	author = {Nathaniel M. Evans and Mark T. Holder and Marcos S. Barbeitos and
	Beth Okamura and Paulyn Cartwright},
	title = {The Phylogenetic Position of {Myxozoa}: Exploring Conflicting Signals
	in Phylogenomic and Ribosomal Data Sets},
	journal = {Molecular Biology and Evolution},
	year = {2010},
	volume = {27},
	pages = {2733--2746},
	number = {12},
	month = {Dec},
	doi = {10.1093/molbev/msq159},
	rating = {0},
	url = {http://mbe.oxfordjournals.org/content/27/12/2733.full?sid=3dce9a83-c059-4046-8e05-84be548051d9}
	}
@ARTICLE{GelfandEtAl2006,
	author = {Alan E Gelfand and Silander, Jr., John A. and {Shan-shan} Wu and
	Andrew M. Latimer and Paul O. Lewis and Anthony G. Rebelo and Mark
	Holder},
	title = {Explaining Species Distribution Patterns through Hierarchical Modeling},
	journal = {{B}ayesian Analysis},
	year = {2006},
	volume = {1},
	pages = {41-92},
	url = {http://ba.stat.cmu.edu/journal/2006/vol01/issue01/gelfand.pdf}
	}
@ARTICLE{HeathHH2012,
	author = {Tracy A. Heath and Mark T. Holder and John P. Huelsenbeck},
	title = {A {Dirichlet} Process Prior for Estimating Lineage-Specific Substitution
	Rates.},
	journal = {Molecular Biology and Evolution},
	year = {2012},
	volume = {29},
	pages = {939-955},
	number = {3},
	doi = {10.1093/molbev/msr255},
	url = {http://mbe.oxfordjournals.org/content/early/2011/11/04/molbev.msr255.abstract}
	}
@INCOLLECTION{HillisHolder2000,
	author = {David M. Hillis and Mark T. Holder},
	title = {Reconstructing the Tree of Life},
	booktitle = {New Technologies for the Life Sciences: A Trends Guide.},
	publisher = {Elsevier},
	year = {2000},
	volume = {{\em Supplement to Trends Journals}},
	pages = {47-50},
	date-modified = {2011-10-05 11:47:30 -0500}
	}
@ARTICLE{HolderEtAl1994,
	author = {Holder, DA and Arevalo, E. and Holder, MT and Taylor, JF and Davis,
	SK},
	title = {Bovine microsatellite dinucleotide repeat polymorphisms at the TEXAN-1,
	TEXAN-2, TEXAN-3, TEXAN-4 and TEXAN-5 loci},
	journal = {Animal Genetics},
	year = {1994},
	volume = {25},
	pages = {201--201},
	number = {3},
	doi = {10.1111/j.1365-2052.1994.tb00123.x},
	publisher = {Wiley Online Library},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2052.1994.tb00123.x/abstract}
	}
@INCOLLECTION{HolderH2007,
	author = {Kristina Kichler Holder and Mark T. Holder},
	title = {Phylogeography and Population Genetics},
	booktitle = {Biology and Conservation of {R}idley Sea Turtles},
	publisher = {Johns Hopkins University Press},
	year = {2007},
	editor = {Pamela T. Plotkin},
	pages = {107--118}
	}
@ARTICLE{HolderAndersonHolloway2001,
	author = {Mark T. Holder and Jennifer A. Anderson and Alisha K. Holloway},
	title = {Difficulties in Detecting Hybridization},
	journal = {Systematic Biology},
	year = {2001},
	volume = {50},
	pages = {978-982},
	number = {6},
	doi = {10.1080/106351501753462911},
	url = {http://sysbio.oxfordjournals.org/cgi/reprint/50/6/978}
	}
@ARTICLE{HolderEtAl1999,
	author = {Mark T. Holder and Mark V. Erdmann and Thomas P. Wilcox and Roy L.
	Caldwell and David M. Hillis},
	title = {Two living species of coelacanths?},
	journal = {Proceedings of the National Academy of Sciences},
	year = {1999},
	volume = {96},
	pages = {12616-12620},
	number = {22},
	doi = {10.1073/pnas.96.22.12616},
	url = {http://www.pnas.org/content/96/22/12616.short}
	}
@ARTICLE{HolderLewis2003,
	author = {Mark T. Holder and Paul O. Lewis},
	title = {Phylogeny Estimation: Traditional and {B}ayesian Approaches},
	journal = {Nature Reviews Genetics},
	year = {2003},
	volume = {43},
	pages = {275-284},
	doi = {10.1038/nrg1044},
	url = {http://www.nature.com/nrg/journal/v4/n4/full/nrg1044.html}
	}
@ARTICLE{HolderLS2010,
	author = {Mark T. Holder and Paul O. Lewis and David L. Swofford},
	title = {The {Akaike} Information Criterion Will Not Choose the No Common
	Mechanism Model},
	journal = {Systematic Biology},
	year = {2010},
	volume = {59},
	pages = {477-485},
	number = {4},
	month = {Jul},
	doi = {10.1093/sysbio/syq028},
	rating = {0},
	url = {http://sysbio.oxfordjournals.org/cgi/content/full/59/4/477}
	}
@ARTICLE{HolderLewisSwoffordLarget2005,
	author = {Mark T. Holder and Paul O. Lewis and David L. Swofford and Bret Larget},
	title = {Hastings Ratio of the LOCAL Proposal Used in {B}ayesian Phylogenetics},
	journal = {Systematic Biology},
	year = {2005},
	volume = {54},
	pages = {961-965},
	doi = {10.1080/10635150500354670},
	issue = {6},
	url = {http://sysbio.oxfordjournals.org/cgi/content/full/54/6/961}
	}
@ARTICLE{HolderS2011,
	author = {Mark T. Holder and Mike Steel},
	title = {Estimating phylogenetic trees from pairwise likelihoods and posterior
	probabilities of substitution counts},
	journal = {Journal of Theoretical Biology},
	year = {2011},
	volume = {280},
	pages = {159--166},
	number = {1},
	month = {July},
	doi = {10.1016/j.jtbi.2011.04.005},
	url = {http://www.sciencedirect.com/science/article/B6WMD-52MY688-1/2/8e287b6af19b84e35bdf3d9e7e0d1a3f}
	}
@INCOLLECTION{HolderSB2010,
	author = {Mark T. Holder and Jeet Sukumaran and Rafe M. Brown},
	title = {Recent Developments in {B}ayesian Phylogenetics},
	booktitle = {Bayesian Modeling in Bioinformatics},
	publisher = {Chapman \& Hall/CRC},
	year = {2010},
	editor = {Dipak K. Dey and Samiran Ghosh and Bani K. Mallick},
	pages = {193-232},
	date-modified = {2010-11-18 15:28:07 -0600}
	}
@ARTICLE{HolderSL2008,
	author = {Mark T. Holder and Jeet Sukumaran and Paul O. Lewis},
	title = {A justification for reporting majority-rule consensus tree in {B}ayesian
	phylogenetics},
	journal = {Systematic Biology},
	year = {2008},
	volume = {57},
	pages = {814-821},
	number = {5},
	doi = {10.1080/10635150802422308},
	url = {http://sysbio.oxfordjournals.org/cgi/content/full/57/5/814}
	}
@ARTICLE{HolderZD2008,
	author = {Mark T. Holder and Derrick J. Zwickl and Christophe Dessimoz},
	title = {Evaluating the Robustness of Phylogenetic Methods to Among-Site Variability
	in Substitution Processes},
	journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
	year = {2008},
	volume = {363},
	pages = {4013-4012},
	doi = {10.1098/rstb.2008.0162},
	url = {http://rstb.royalsocietypublishing.org/content/363/1512/4013}
	}
@ARTICLE{KichlerEtAl1999,
	author = {Kristina L. Kichler and Mark T. Holder and Scott K. Davis and Rene
	Marquez and David Owens},
	title = {Detection of multiple paternity in the {K}emp's ridley sea turtle
	with limited sampling},
	journal = {Molecular Ecology},
	year = {1999},
	volume = {8},
	pages = {819-830},
	doi = {10.1046/j.1365-294X.1999.00635.x},
	url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1365-294X.1999.00635.x/abstract}
	}
@ARTICLE{KochH2012,
	author = {Jordan M. Koch and Mark T. Holder},
	title = {An Algorithm for Calculating the Probability of Classes of Data Patterns
	on a Genealogy},
	journal = {PLOS Currents Tree of Life},
	year = {2012},
	volume = {Dec 14 [last modified: 2012 Dec 14]},
	number = {1},
	doi = {10.1371/4fd1286980c08},
	url = {http://currents.plos.org/treeoflife/article/an-algorithm-for-calculating-the-probability-of-classes-of-data-patterns-on-a-genealogy}
	}
@ARTICLE{LaknerHGN2011,
	author = {Clemens Lakner and Mark T. Holder and Nick Goldman and Gavin J. P.
	Naylor},
	title = {What's in a Likelihood? Simple Models of Protein Evolution and the
	Contribution of Structurally Viable Reconstructions to the Likelihood},
	journal = {Systematic Biology},
	year = {2011},
	volume = {60},
	pages = {161-174.},
	number = {2},
	doi = {10.1093/sysbio/syq088},
	url = {http://sysbio.oxfordjournals.org/content/60/2/161}
	}
@ARTICLE{LappEtAl2007,
	author = {Hilmar Lapp and Sendu Bala and James P. Balhoff and Amy Bouck and
	Naohisa Goto and Mark Holder and Richard Holland and Alisha Holloway
	and Toshiaki Katayama and Paul O. Lewis and Aaron Mackey and Brian
	I. Osborne and William H. Piel and Sergei L. Kosakovsky Pond and
	Art Poon and Wei-Gang Qiu and Jason E. Stajich and Arlin Stoltzfus
	and Tobias Thierer and Albert J. Vilella and Rutger A. Vos and Christian
	M. Zmasek and Derrick Zwickl and Todd J. Vision},
	title = {The 2006 {NESCent} Phyloinformatics Hackathon: A Field Report},
	journal = {Evolutionary Bioinformatics},
	year = {2007},
	volume = {3},
	pages = {357--366},
	url = {http://la-press.com/article.php?article_id=480}
	}
@ARTICLE{LewisHolderHolsinger2005,
	author = {Paul O. Lewis and Mark T. Holder and Kent E. Holsinger},
	title = {Polytomies and {B}ayesian phylogenetic inference},
	journal = {Systematic Biology},
	year = {2005},
	volume = {54},
	pages = {241--253},
	doi = {10.1080/10635150590924208},
	issue = {2},
	url = {http://sysbio.oxfordjournals.org/cgi/content/full/54/2/241}
	}
@ARTICLE{LiberlesEtAl2012,
	author = {David A. Liberles and Sarah A. Teichmann and Ivet Bahar and Ugo Bastolla
	and Jesse Bloom and Erich Bornberg-Bauer and Lucy J. Colwell and
	A. P. Jason de Koning and Nikolay V. Dokholyan and Julian Echave
	and Arne Elofsson and Dietlind L. Gerloff and Richard A. Goldstein
	and Johan A. Grahnen and Mark T. Holder and Clemens Lakner and Nicholas
	Lartillot and Simon C. Lovell and Gavin Naylor and Tina Perica and
	David D. Pollock and Tal Pupko and Lynne Regan and Andrew Roger and
	Nimrod Rubinstein and Eugene Shakhnovich and Kimmen Sj\"olander and
	Shamil Sunyaev and Ashley I. Teufel and Jeffrey L. Thorne and Joseph
	W. Thornton and Daniel M. Weinreich and Simon Whelan},
	title = {The interface of protein structure, protein biophysics, and molecular
	evolution},
	journal = {Protein Science},
	year = {2012},
	volume = {21},
	pages = {769-785},
	number = {6},
	doi = {10.1002/pro.2071},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/pro.2071/abstract}
	}
@ARTICLE{LiuWHNYSL2011,
	author = {Kevin Liu and Tandy J. Warnow and Mark T. Holder and Serita Nelesen
	and Jiaye Yu and Alexandros Stamatakis and C. Randal Linder},
	title = {{SAT{\'e}-II}: Very Fast and Accurate Simultaneous Estimation of
	Multiple Sequence Alignments and Phylogenetic Trees},
	journal = {Systematic Biology},
	year = {2012},
	volume = {61},
	pages = {90-106},
	number = {1},
	doi = {10.1093/sysbio/syr095},
	url = {http://sysbio.oxfordjournals.org/content/61/1/90.full}
	}
@ARTICLE{OaksEtAl2012,
	author = {Jamie R. Oaks and Jeet Sukumaran and Jacob A. Esselstyn and Charles
	W. Linkem and Cameron D. Siler and Mark T. Holder and Rafe M. Brown},
	title = {Evidence for climate-driven diversification? A caution for interpreting
	{ABC} inferences of simultaneous historical events},
	journal = {Evolution},
	year = {2013},
	volume = {67},
	pages = {991-1010},
	doi = {10.1111/j.1558-5646.2012.01840.x},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.2012.01840.x/full}
	}
@ARTICLE{PetersonH2012,
	author = {A. Townsend Peterson and Mark T. Holder},
	title = {Phylogenetic Assessment of {Filoviruses}: How Many Lineages of {Marburvirus}?},
	journal = {Ecology and Evolution},
	year = {2012},
	volume = {2},
	pages = {1826-1833},
	number = {8},
	doi = {10.1002/ece3.297},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/ece3.297/full}
	}
@ARTICLE{PetersonKGSH2010,
	author = {A. Townsend Peterson and Sandra Knapp and Robert Guralnick and Jorge
	Sober{\'o}n and Mark T. Holder},
	title = {The big questions for biodiversity informatics},
	journal = {Systematics and Biodiversity},
	year = {2010},
	volume = {8},
	pages = {159--168},
	number = {2},
	doi = {10.1080/14772001003739369},
	keywords = {analysis, biodiversity data capture, data integration, ecology, evolutionary
	biology, informatics, interpretation, phylogeny},
	url = {http://www.informaworld.com/smpp/content~db=all~content=a923302569~frm=abslink}
	}
@ARTICLE{SukumaranH2011,
	author = {Jeet Sukumaran and Mark T. Holder},
	title = {{Ginkgo}: spatially-explicit simulator of complex phylogeographic
	histories},
	journal = {Molecular Ecology Resources},
	year = {2011},
	volume = {11},
	pages = {364-369},
	number = {2},
	doi = {10.1111/j.1755-0998.2010.02926.x},
	rating = {0},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1755-0998.2010.02926.x/abstract}
	}
@ARTICLE{SukumaranH2010,
	author = {J Sukumaran and Mark T. Holder},
	title = {{DendroPy}: a {Python} library for phylogenetic computing},
	journal = {Bioinformatics},
	year = {2010},
	volume = {26},
	pages = {1569--1571},
	number = {12},
	doi = {10.1093/bioinformatics/btq228},
	rating = {0},
	url = {http://bioinformatics.oxfordjournals.org/content/26/12/1569.abstract}
	}
@ARTICLE{NEXML,
	author = {Rutger A. Vos and James P. Balhoff and Jason Caravas and Mark T.
	Holder and Hilmar Lapp and Wayne~P. Maddison and Peter~E. Midford
	and Anurag Priyam and Jeet Sukumaran and Xuhua Xia and Arlin Stoltzfus},
	title = {{NeXML:} rich, extensible, and verifiable representation of comparative
	data and metadata},
	journal = {Systematic Biology},
	year = {2012},
	volume = {61},
	pages = {675--689},
	number = {4},
	doi = {10.1093/sysbio/sys025},
	url = {http://sysbio.oxfordjournals.org/content/61/4/675}
	}
@ARTICLE{ZwicklHolder2005,
	author = {Derrick J. Zwickl and Mark T. Holder},
	title = {Model Parameterization, Prior Distributions and the General Time-Reversible
	Model in {B}ayesian Phylogenetics},
	journal = {Systematic Biology},
	year = {2004},
	volume = {53},
	pages = {877-888},
	doi = {10.1080/10635150490522584},
	issue = {6},
	url = {http://sysbio.oxfordjournals.org/cgi/content/full/53/6/877}
	}