phylo.bio.ku.edu

Holder MT, Lewis PO, Swofford DL.  2010.  The Akaike Information Criterion Will Not Choose the No Common Mechanism Model. Systematic Biology. 59(4):477-485.

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Ayres DL, Darling A, Zwickl DJ, Beerli P, Holder MT, Lewis PO, Huelsenbeck JP, Ronquist F, Swofford DL, Cummings MP et al..  2012.  BEAGLE: an Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics. Systematic Biology. 61(1):170-173.

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Peterson TA, Knapp S, Guralnick R, Soberón J, Holder MT.  2010.  The big questions for biodiversity informatics. Systematics and Biodiversity. 8:159–168.

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Sukumaran J, Holder MT.  2010.  DendroPy: A Python library for phylogenetic computing. Bioinformatics. 26:1569-1571.

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Holder MT, Anderson JA, Holloway AK.  2001.  Difficulties in Detecting Hybridization. Systematic Biology. 50:978-982.

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Heath TA, Holder MT, Huelsenbeck JP.  2012.  A Dirichlet Process Prior for Estimating Lineage-Specific Substitution Rates. Molecular Biology and Evolution. 29(3):939-955.

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Holder MT, Steel M.  2011.  Estimating phylogenetic trees from pairwise likelihoods and posterior probabilities of substitution counts. Journal of Theoretical Biology. 280(1):159-166.

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Holder MT, Zwickl DJ, Dessimoz C.  2008.  Evaluating the Robustness of Phylogenetic Methods to Among-Site Variability in Substitution Processes. Philosophical Transactions of the Royal Society B: Biological Sciences. 363:4013-4012.

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Sukumaran J, Holder MT.  2011.  Ginkgo: spatially-explicit simulator of complex phylogeographic histories. Molecular Ecology Resources. 11(2):364-369.

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Holder MT, Lewis PO, Swofford DL, Larget B.  2005.  Hastings Ratio of the LOCAL Proposal Used in Bayesian Phylogenetics. Systematic Biology. 54:961-965.

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Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning JAP, Dokholyan NV, Echave J et al..  2012.  The interface of protein structure, protein biophysics, and molecular evolution. Protein Science. 21:769-785.

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Holder MT, Sukumaran J, Lewis PO.  2008.  A justification for reporting majority-rule consensus tree in Bayesian phylogenetics. Systematic Biology. 57:814-821.

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Zwickl DJ, Holder MT.  2004.  Model Parameterization, Prior Distributions and the General Time-Reversible Model in Bayesian Phylogenetics. Systematic Biology. 53:877-888.

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Vos RA, Balhoff JP, Caravas J, Holder MT, Lapp H, Maddison WP, Midford P, Priyam A, Sukumaran J, Xia X et al..  2012.  NeXML: rich, extensible, and verifiable representation of comparative data and metadata. Systematic Biology. 61(4):675-689.

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Peterson TA, Holder MT.  2012.  Phylogenetic Assessment of Filoviruses: How Many Lineages of Marburvirus? Ecology and Evolution. 2(8):1826-1833.

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Lewis PO, Holder MT, Holsinger KE.  2005.  Polytomies and Bayesian phylogenetic inference. Systematic Biology. 54:241–253.

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Hillis DM, Holder MT.  2000.  Reconstructing the Tree of Life. New Technologies for the Life Sciences: A Trends Guide. Supplement to Trends Journals. :47-50.

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Liu K, Warnow TJ, Holder MT, Nelesen S, Yu J, Stamatakis A, Linder RC.  2012.  SATé-II: Very Fast and Accurate Simultaneous Estimation of Multiple Sequence Alignments and Phylogenetic Trees. Systematic Biology. 61(1):90-106.

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Lakner C, Holder MT, Goldman N, Naylor GJP.  2011.  What's in a Likelihood? Simple Models of Protein Evolution and the Contribution of Structurally Viable Reconstructions to the Likelihood Systematic Biology. 60(2):161-174.

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Koch JM, Holder MT.  2012.  An Algorithm for Calculating the Probability of Classes of Data Patterns on a Genealogy. PLOS Currents Tree of Life.

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