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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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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, Erdmann MV, Wilcox TP, Caldwell RL, Hillis DM.  1999.  Two living species of coelacanths? Proceedings of the National Academy of Sciences. 96:12616-12620.
Holder KK, Holder MT.  2007.  Phylogeography and Population Genetics. Biology and Conservation of {R}idley Sea Turtles. :107–118.
Holder MT, Lewis PO.  2003.  Phylogeny Estimation: Traditional and Bayesian Approaches. Nature Reviews Genetics. 43:275-284.
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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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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.
Alfaro ME, Holder MT.  2006.  The Posterior and the Prior in Bayesian Phylogenetics. Annual Review of Ecology, Evolution, and Systematics. 37:19-42.