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

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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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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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