ProteinEvolver generates samples of protein-coding genes and protein sequences evolved along phylogenies under structure-based substitution models. These models consider the protein structure to evaluate candidate mutations, which can be accepted (substitutions) or rejected depending on the energy of the protein structure of the mutated sequence.
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Bioinformatics. 2013 Dec 1;29(23):3020-8. doi: 10.1093/bioinformatics/btt530. Epub 2013 Sep 12.
Protein evolution along phylogenetic histories under structurally constrained substitution models.
Arenas M1, Dos Santos HG, Posada D, Bastolla U.