ProteinEvolver CAN NOW BE FOUND AT https://github.com/MiguelArenas/proteinevolver

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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. The simulation of molecular evolution occurs along phylogenetic histories, which can be either user-specified or simulated by the coalescent modified with recombination (including recombination hotspots), migration, demographics and longitudinal sampling.

Arenas, M.; Dos Santos, H.G.; Posada, D. and Bastolla, U. 2013. Protein Evolution along Phylogenetic Histories under Structurally Constrained Substitution Models. Bioinformatics, 29(23):3020-3028.

http://bioinformatics.oxfordjournals.org/content/29/23/3020.abstract

Please, do not hesitate to contact us (miguelmmmab@gmail.com) for any question.