GSR: Simulator - ProteinEvolver

Basic Package Attributes
AttributeValue
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 7 years, 11 months ago
Homepagehttp://code.google.com/p/proteinevolver/
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 (1 days ago)
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataDiploid DNA Sequence, Haploid DNA Sequence, Protein Sequence,
VariationsSingle Nucleotide Variation, Amino acid variation,
Simulation MethodStandard Coalescent, Exact Coalescent, Phylogenetic,
Input
Data TypeEmpirical, Ancestral Sequence, Other,
File format
Output
Data TypeDemographic, Mutation,
Sequencing Reads
File FormatFasta or Fastq, Phylip, NEXUS,
Sample TypeLongitudinal,
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size ChangesConstant Size, Exponential Growth or Decline, Logistic Growth, Bottleneck,
Gene FlowStepping Stone Models, Island Models, Continent-Island Models,
Spatiality
Life CycleUser-Defined transition matrices,
Mating System
Fecundity
Natural Selection
Determinant
Models
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,
Other
InterfaceCommand-line,
Development
Tested PlatformsMac OS X, Linux and Unix,
LanguageC or C++,
LicenseGNU Public License,
GSR Certification

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