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GSR: Simulator - CastNet
| Attribute | Value |
|---|---|
| Title | CastNet |
| Short Description | a systems-level sequence evolution simulator |
| Long Description | CastNet is a genome evolution simulator that assumes each genome is a collection of genes with constantly evolving regulatory interactions in between them. The regulatory interactions produce a phenotype in the form of gene expression profiles, upon which fitness is calculated. A genetic algorithm is then used to evolve a population of such entities through a user-defined phylogeny. Importantly, the regulatory mutations are a response to sequence mutations, thus making a 1-1 relationship between the rate of evolution of sequences and of regulatory parameters. |
| Keywords | Coevolution; Coevolutionary webs; Complex systems; Evo-devo; Evolution simulation; Evolutionary systems; Gene regulatory networks. |
| Project Started | 2023 |
| Homepage | https://github.com/carlosj-rr/CastNet |
| Citations | |
| GSR Certification | This simulator has not yet been evaluated for GSR Certification. Learn more about or request GSR Certification. |
| 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 | |
| Input | |
| Data Type | |
| File format | |
| Output | |
| Data Type | Genotype or Sequence, Phylogenetic Tree, |
| Sequencing Reads | |
| File Format | Fasta or Fastq, |
| Sample Type | |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | |
| Gene Flow | |
| Spatiality | |
| Life Cycle | |
| Mating System | |
| Fecundity | |
| Natural Selection | |
| Determinant | |
| Models | |
| Recombination | |
| Mutation Models | |
| Events Allowed | |
| Other | |
| Interface | Command-line, |
| Development | |
| Tested Platforms | Windows, Mac OS X, Linux and Unix, |
| Language | Python, |
| License | GNU Public License, |
| GSR Certification |
Number of Primary Citations: 0
Number of Non-Primary Citations: 1
The following 1 publications are selected examples of applications that used CastNet.
2023
Rivera-Rivera CJ, Grbic D, CastNet: a systems-level sequence evolution simulator., BMC Bioinformatics, June 12, 2023 [Abstract]