GSR: Simulator - GppFst

Basic Package Attributes
AttributeValue
Title GppFst
Short Description GppFst is an open source R package that generates posterior predictive distributions of Fst and day under a neutral coalescent model to identify putative targets of selection from genomic data.
Long Description GppFst is a posterior predictive simulation (PPS) framework to generate theoretical distributions of FST and dXY under the neutral coalescent model for two populations that accounts for demographic parameters in a probabilistic framework. Importantly, our method allows users to explicitly test the null hypothesis of genetic drift when conducting genomic scans. PPS is a popular method for evaluating model fit within a Bayesian framework that has been used to test a variety of evolutionary models (Gelman et al., 2004; Reid et al., 2014). GppFst explicitly accounts for the demographic history of two genetically-isolated species, including multiple demographic and experimental parameters (and uncertainty in those parameters), such as sample sizes, demographic parameters, unequal rates of genetic drift within populations (unequal s), and divergence time. Our method allows users to simulate theoretical distributions that are conditioned on sampling multiple linked SNPs per locus – allowing users to take full advantage of large genomic datasets. We provide our PPS model in the package GppFst (Genomic Posterior Predictive distributions of FST), which offers a user-friendly, open-source framework to generate theoretical distributions of FST and dXY under the neutral coalescent model.
Version 0.1.2
Project Started 2016
Last Release 4 years, 1 month ago
Homepagehttps://github.com/radamsRHA/GppFst
Citations Richard Adams, Drew Schield, Daren Card, Heath Blackmon, and Todd Castoe, GppFst Genomic posterior predictive simulations of FST and dXY for identifying outlier loci from population genomic data, Bioinformatics; In Review, 09-20-2016
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Last evaluated10-08-2019 (375 days ago)
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 MethodStandard Coalescent,
Input
Data TypeEmpirical, Other,
File formatOther,
Output
Data Type
Sequencing ReadsOther,
File FormatOther,
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
LanguageR,
License
GSR CertificationAccessibility,

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