GSR: Simulator - SpartaABC

Basic Package Attributes
AttributeValue
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 4 years, 6 months ago
Homepagehttp://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, 07-03-2017 [ Abstract, cited in PMC ]
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Author verificationThe 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.
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated Data
Variations
Simulation Method
Input
Data Type
File format
Output
Data Type
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
Development
Tested Platforms
Language
License
GSR Certification

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