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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.
  • Version: 1.0
  • Usage and installation : Documentation included with the package.
  • Examples: included with the package.
  • Free use for Educational and Research Purposes.
  • Download: Google Code.
  • Reference: Arenas, M.; Dos Santos, H.G.; Posada, D. and Bastolla, U. (2013) Bioinformatics, 29(23):3020-3028.
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