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Journal Article
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.
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.
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.
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.
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.
Holder MT, Lewis PO, Swofford DL, Larget B.  2005.  Hastings Ratio of the LOCAL Proposal Used in Bayesian Phylogenetics. Systematic Biology. 54:961-965.
Holder MT, Sukumaran J, Lewis PO.  2008.  A justification for reporting majority-rule consensus tree in Bayesian phylogenetics. Systematic Biology. 57:814-821.
Holder MT, Lewis PO.  2003.  Phylogeny Estimation: Traditional and Bayesian Approaches. Nature Reviews Genetics. 43:275-284.
Lewis PO, Holder MT, Holsinger KE.  2005.  Polytomies and Bayesian phylogenetic inference. Systematic Biology. 54:241–253.