GSR: Simulator - ProteinEvolver

Basic Package Attributes
Title ProteinEvolver
Short Description Simulation of protein evolution along phylogenies under structure-based substitution models
Long Description 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 1.2.0.
Project Started 2013
Last Release 8 years, 8 months ago
Citations Arenas M, Dos Santos HG, Posada D, Bastolla U, Protein evolution along phylogenetic histories under structurally constrained substitution models., Bioinformatics, 12-01-2013 [ Abstract, cited in PMC ]
GSR Certification This package has been evaluated. No certificates were awarded at this time.
Last evaluated11-05-2020 (320 days ago)
Detailed Attributes
Attribute CategoryAttribute
Type of Simulated DataDiploid DNA Sequence, Haploid DNA Sequence, Protein Sequence,
VariationsSingle Nucleotide Variation, Amino acid variation,
Simulation MethodStandard Coalescent, Exact Coalescent, Phylogenetic,
Data TypeEmpirical, Ancestral Sequence, Other,
File format
Data TypeDemographic, Mutation,
Sequencing Reads
File FormatFasta or Fastq, Phylip, NEXUS,
Sample TypeLongitudinal,
Trait Type
Evolutionary Features
Population Size ChangesConstant Size, Exponential Growth or Decline, Logistic Growth, Bottleneck,
Gene FlowStepping Stone Models, Island Models, Continent-Island Models,
Life CycleUser-Defined transition matrices,
Mating System
Natural Selection
RecombinationUniform, Varying Recombination Rates,
Mutation ModelsMarkov DNA Evolution Models, Codon and Amino Acid Models, Others,
Events AllowedPopulation Merge and Split, Varying Demographic Features, Population Events, Varying Genetic Features,
Tested PlatformsMac OS X, Linux and Unix,
LanguageC or C++,
LicenseGNU Public License,
GSR Certification

The following 1 publications are selected examples of applications that used ProteinEvolver.


Facco E, Pagnani A, Russo ET, Laio A, The intrinsic dimension of protein sequence evolution., PLoS Comput Biol, 04-08-2019 [Abstract]

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