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GSR: Simulator - SpartaABC
| Attribute | Value |
|---|---|
| Title | SpartaABC |
| Short Description | a web server to simulate sequences with indel parameters inferred using an approximate Bayesian computation algorithm |
| Long Description | SpartaABC is an Approximate Bayesian Computation (ABC) reject algorithm to infer indel parameters from sequence data. It focuses on the inference of three indel parameters: IR — the indel-to-substitution rate ratio, A — the shape parameter for the power law distribution controlling the indel length, and RL — the root length parameter. SpartaABC extracts a vector of summary statistics from its input; it then performs repeated simulations using an integrated sequence simulator (Fletcher and Yang 2009, Cartwright 2016) under various indel parameters. From each such simulated dataset it extracts a vector of summary statistics and computes its distance from the vector extracted for the input using a weighted Euclidean distance. |
| Version | 1.0 |
| Last Release | 8 years, 7 months ago |
| Homepage | http://spartaabc.tau.ac.il/webserver |
| Citations | Ashkenazy H, Levy Karin E, Mertens Z, Cartwright RA, Pupko T, SpartaABC: a web server to simulate sequences with indel parameters inferred using an approximate Bayesian computation algorithm., Nucleic Acids Res, July 3, 2017 [ Abstract, cited in PMC ] |
| GSR Certification | ✔ Accessibility |
| Last evaluated | April 24, 2023 (874 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 | Genotype at Genetic Markers, |
| Variations | Insertion and Deletion, |
| Simulation Method | Other, |
| Input | |
| Data Type | Ancestral Sequence, |
| File format | |
| Output | |
| Data Type | Genotype or Sequence, |
| Sequencing Reads | |
| File Format | |
| 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 | Web-based, |
| Development | |
| Tested Platforms | |
| Language | C or C++, |
| License | |
| GSR Certification | Accessibility, Documentation, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 0
No example publication using SpartaABC has been provided.
Please propose new citations if you are aware of publications that use this software.