GSR: Simulator - ProteinEvolver
Attribute | Value |
---|---|
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 | 11 years, 2 months ago |
Homepage | http://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 | ✔ Accessibility |
Last evaluated | 05-15-2023 (312 days ago) |
Attribute Category | Attribute |
---|---|
Target | |
Type of Simulated Data | Diploid DNA Sequence, Haploid DNA Sequence, Protein Sequence, |
Variations | Single Nucleotide Variation, Amino acid variation, |
Simulation Method | Standard Coalescent, Exact Coalescent, Phylogenetic, |
Input | |
Data Type | Empirical, Ancestral Sequence, Other, |
File format | |
Output | |
Data Type | Demographic, Mutation, |
Sequencing Reads | |
File Format | Fasta or Fastq, Phylip, NEXUS, |
Sample Type | Longitudinal, |
Phenotype | |
Trait Type | |
Determinants | |
Evolutionary Features | |
Demographic | |
Population Size Changes | Constant Size, Exponential Growth or Decline, Logistic Growth, Bottleneck, |
Gene Flow | Stepping Stone Models, Island Models, Continent-Island Models, |
Spatiality | |
Life Cycle | User-Defined transition matrices, |
Mating System | |
Fecundity | |
Natural Selection | |
Determinant | |
Models | |
Recombination | Uniform, Varying Recombination Rates, |
Mutation Models | Markov DNA Evolution Models, Codon and Amino Acid Models, Others, |
Events Allowed | Population Merge and Split, Varying Demographic Features, Population Events, Varying Genetic Features, |
Other | |
Interface | Command-line, |
Development | |
Tested Platforms | Mac OS X, Linux and Unix, |
Language | C or C++, |
License | GNU Public License, |
GSR Certification | Accessibility, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 2
The following 2 publications are selected examples of applications that used ProteinEvolver.
2023
Del Amparo R, González-Vázquez LD, Rodríguez-Moure L, Bastolla U, Arenas M, Consequences of Genetic Recombination on Protein Folding Stability., J Mol Evol, 02-01-2023 [Abstract]
2019
Facco E, Pagnani A, Russo ET, Laio A, The intrinsic dimension of protein sequence evolution., PLoS Comput Biol, 04-08-2019 [Abstract]