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GSR: Simulator - Serial NetEvolve
| Attribute | Value |
|---|---|
| Title | Serial NetEvolve |
| Short Description | A flexible utility for generating serially-sampled sequences along a tree or recombinant network |
| Long Description | Serial NetEvolve is a modification of the Treevolve program in which serially sampled sequences are evolved along a randomly generated coalescent tree or network (Grassly et al. 1999; Hudson 1983; Kingman 1982) . Treevolve offers a variety of evolutionary model and population parameters including a rate of recombination and as such it was chosen over other programs to be adapted for the simulation of serially sampled data. The new features include the choice of either a clock-like model of evolution or a variable rate of evolution, simulation of serial samples and the output of the randomly generated tree or network in Newick format or in our newly formulated NeTwick format. |
| Version | 1.0 |
| Project Started | 2006 |
| Last Release | 17 years, 9 months ago |
| Homepage | https://biorg.cis.fiu.edu/SNE/index.htm |
| Citations | Buendia P, Narasimhan G, Serial NetEvolve: a flexible utility for generating serially-sampled sequences along a tree or recombinant network., Bioinformatics, 09-15-2006 [ Abstract, cited in PMC ] |
| GSR Certification | ✔ Accessibility |
| Last evaluated | 05-15-2023 (334 days ago) |
| Author verification | The basic description provided was derived from a website or publications by the GSR team and has not yet been verified by the simulation author. To modify this entry or add more information, propose changes to this simulator. |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Haploid DNA Sequence, |
| Variations | Biallelic Marker, |
| Simulation Method | Standard Coalescent, |
| Input | |
| Data Type | |
| File format | Phylip, |
| Output | |
| Data Type | Genotype or Sequence, Phenotypic Trait, |
| Sequencing Reads | |
| File Format | |
| Sample Type | |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | Constant Size, Exponential Growth or Decline, |
| Gene Flow | Island Models, |
| Spatiality | |
| Life Cycle | |
| Mating System | Random Mating, |
| Fecundity | |
| Natural Selection | |
| Determinant | |
| Models | |
| Recombination | Varying Recombination Rates, |
| Mutation Models | Markov DNA Evolution Models, |
| Events Allowed | |
| Other | |
| Interface | Command-line, Graphical User Interface, |
| Development | |
| Tested Platforms | Windows, Linux and Unix, |
| Language | C or C++, |
| License | GNU Public License, |
| GSR Certification | Accessibility, Documentation, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 0
No example publication using Serial NetEvolve has been provided.
Please propose new citations if you are aware of publications that use this software.