phylo.bio.ku.edu

Lapp H, Bala S, Balhoff JP, Bouck A, Goto N, Holder MT, Holland R, Holloway A, Katayama T, Lewis PO et al..  2007.  The 2006 NESCent Phyloinformatics Hackathon: A Field Report. Evolutionary Bioinformatics. 3:357–366.

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Grismer LL, Neang T, Chav T, Perry L. Wood J, Oaks JR, Holden J, Grismer JL, Szutz TR, Youmans TM.  2008.  Additional amphibians and reptiles from the Phnom Samkos Wildlife Sanctuary in Northwestern Cardamom Mountains, Cambodia, with comments on their taxonomy and the discovery of four new species. Raffles Bulletin of Zoology. 56:161-175.

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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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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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Sukumaran J.  2002.  The amphibian fauna of a forested area in Temengor, Northern Peninsular Malaysia. Hamadryad. 27:1–10.

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Hillis DM, Heath TA, StJohn K.  2005.  Analysis and Visualization of Tree Space. Systematic Biology. 54:471-482.

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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, Linkem CW.  2009.  Choice of topology estimators in Bayesian phylogenetic analysis. Molecular Biology and Evolution. 26:1–3.

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

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Kichler KL, Holder MT, Davis SK, Marquez R, Owens D.  1999.  Detection of multiple paternity in the Kemp's ridley sea turtle with limited sampling. Molecular Ecology. 8:819-830.

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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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Allman ES, Holder MT, Rhodes JA.  2010.  Estimating trees from filtered data: Identifiability of models for morphological phylogenetics. Journal of Theoretical Biology. 263(1):108-119.

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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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Wiens J, Sukumaran J, Pyron A, Brown RM.  2009.  Evolutionary and biogeographic origins of high tropical diversity in Old World frogs (Ranidae). Evolution. 63:1217–1231.

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Gelfand AE, Silander, Jr. JA, Wu S-shan, Latimer AM, Lewis PO, Rebelo AG, Holder MT.  2006.  Explaining Species Distribution Patterns through Hierarchical Modeling. {B}ayesian Analysis. 1:41-92.

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Brauer MJ, Holder MT, Dries LA, Zwickl DJ, Lewis PO, Hillis DM.  2002.  Genetic Algorithms and Parallel Processing in Maximum-Likelihood Phylogeny Inference. Molecular Biology and Evolution. 19:1717-1726.

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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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Sukumaran J, Yaakob N, Yong D.  2006.  The herpetofauna of the Southeast Pahang peat-swamp forests. Hamadryad. 30:75–91.

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Zwickl DJ, Hillis DM.  2002.  Increased taxon sampling greatly reduces phylogenetic error. SYSTEMATIC BIOLOGY. 51:588-598. Abstract

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Pollock DD, Zwickl DJ, McGuire JA, Hillis DM.  2002.  Increased taxon sampling is advantageous for phylogenetic inference. SYSTEMATIC BIOLOGY. 51:664-671.

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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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Yaakob N, Sukumaran J.  2006.  An inventory of the amphibians of Pasoh Forest Reserve, Negeri Sembilan, Peninsular Malaysia. Hamadryad. 30:102–107.

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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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Oaks JR, Daul JM, Adler GH.  2008.  Life span of a tropical forest rodent, \emphProechimys semispinosus}. Journal of Mammology. 89:904-908.

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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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Zakon HH, Zwickl DJ, Lu Y, Hillis DM.  2008.  Molecular evolution of communication signals in electric fish. JOURNAL OF EXPERIMENTAL BIOLOGY. 211:1814-1818. Abstract

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Brown RM, Richards S, Sukumaran J, Fougopoulos J.  2006.  A new morphologically cryptic species of forest frog (genus Platymantis) from New Britain Island, Bismarck Archipelago. Zootaxa. 1334:45–68.

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Das I, Yaakob N, Sukumaran J.  2007.  A new species of Microhyla (Anura: Microhylidae) from the Malay Peninsula. Hamadryad. 31:304–314.

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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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Evans NM, Holder MT, Barbeitos MS, Okamura B, Cartwright P.  2010.  The Phylogenetic Position of Myxozoa: Exploring Conflicting Signals in Phylogenomic and Ribosomal Data Sets. Molecular Biology and Evolution. 27:2733–2746.

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Matsui M, Tominaga A, Liu W, Khonsue W, Grismer LL, Diesmos AC, Das I, Sudin A, Yambun P, Yong H et al..  2010.  Phylogenetic relationships of Ansonia from Southeast Asia inferred from mitochondrial DNA sequences: Systematic and biogeographic implications (Anura: Bufonidae). Molecular Phylogenetics and Evolution. 54:561-570.

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Wilcox TP, Zwickl DJ, Heath TA, Hillis DM.  2002.  Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support. Molecular Phylogenetics and Evolution. 25:361-71.

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Siler CD, Oaks JR, Esselstyn JA, Diesmos AC, Brown RM.  2010.  Phylogeny and biogeography of Philippine bent-toed geckos (Gekkonidae: Cyrtodactylus) contradict a prevailing model of Pleistocene diversification. Molecular Phylogenetics and Evolution. ::inpress.

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Holder MT, Lewis PO.  2003.  Phylogeny Estimation: Traditional and Bayesian Approaches. Nature Reviews Genetics. 43:275-284.

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Holder KK, Holder MT.  2007.  Phylogeography and Population Genetics. Biology and Conservation of {R}idley Sea Turtles. :107–118.

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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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Alfaro ME, Holder MT.  2006.  The Posterior and the Prior in Bayesian Phylogenetics. Annual Review of Ecology, Evolution, and Systematics. 37:19-42.

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Edgcomb V, Orsi W, Bunge J, Jeon SO, Christen R, Leslin C, Holder M, Taylor GT, Suarez P, Varela R et al..  2011.  Protistan Microbial Observatory in the Cariaco Basin, Caribbean. I. Species richness and endemicity. ISME Journal. 5(8):1344-1356.

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Holder MT, Sukumaran J, Brown RM.  2010.  Recent Developments in Bayesian Phylogenetics. Bayesian Modeling in Bioinformatics. :inpress.

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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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Grismer L, Sukumaran J, Grismer J, Youmans T, Wood P, Johnson R.  2005.  Report on the herpetofauna from the Temengor Forest Reserve, Perak, West Malaysia. Hamadryad. 29:15–35.

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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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Zakon HH, Lu Y, Zwickl DJ, Hillis DM.  2006.  Sodium channel genes and the evolution of diversity in communication signals of electric fishes: Convergent molecular evolution. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 103:3675-3680. Abstract

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Hillis DM, Pollock DD, McGuire JA, Zwickl DJ.  2003.  Is sparse taxon sampling a problem for phylogenetic inference? SYSTEMATIC BIOLOGY. 52:124-126.

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Sukumaran J, Das I, Haas A.  2006.  A synopsis of bioacoustic studies of Anuran amphibians of Borneo. Herpetological Review. 37:288–293.

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Heath TA, Zwickl DJ, Kim J, Hillis DM.  2008.  Taxon sampling affects inferences of macroevolutionary processes from phylogenetic trees. Systematic Biology. 57:160-166.

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Heath TA, Hedtke SM, Hillis DM.  2008.  Taxon sampling and the accuracy of phylogenetic analyses. Journal of Systematics and Evolution. 46:239-257.

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Holder MT, Erdmann MV, Wilcox TP, Caldwell RL, Hillis DM.  1999.  Two living species of coelacanths? Proceedings of the National Academy of Sciences. 96:12616-12620.

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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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