What's in a Likelihood? Simple Models of Protein Evolution and the Contribution of Structurally Viable Reconstructions to the Likelihood

Accounting for Solvent Accessibility and Secondary Structure in Protein Phylogenetics Is Clearly Beneficial

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Macromolecular Modeling with Rosetta

(2008) Rhiju Das et al.   Annual Review of Biochemistry

An Improved General Amino Acid Replacement Matrix

(2008) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bayesian analysis of amino acid substitution models

(2008) J. P Huelsenbeck et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Basing population genetic inferences and models of molecular evolution upon desired stationary distributions of DNA or protein sequences

(2008) S. C. Choi et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Probabilistic Phylogenetic Inference with Insertions and Deletions

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