GSR: Simulator - FREGENE
Attribute | Value |
---|---|
Title | FREGENE |
Short Description | FREGENE is a C++ program that simulates sequence-like data over large genomic regions in large diploid populations. |
Long Description | FREGENE works forwards-in-time which allows a wide range of demographic and selection scenarios to be implemented. Many such models are already incorporated into FREGENE, and since it is open source users can modify or extend these. Coalescent methods have difficulty incorporating large amounts of gene conversion or crossover (Hoggart et al. 2007), whereas these pose no particular problem for FREGENE. FREGENE offers a flexible model for recombination hotspots, and can readily simulate regions up to tens of Mb on a standard desktop computer. The principle limitation of forward-in-time algorithms is computational, since the entire population must be tracked through time, not only the chromosomes that are ancestral to the observed sample. FREGENE implements many features to enhance computational efficiency, and includes a rescaling option that greatly reduces computation time at the cost of some approximation. |
Project Started | 2007 |
Last Release | 15 years, 8 months ago |
Homepage | http://www.ebi.ac.uk/projects/BARGEN |
Citations | Chadeau-Hyam M, Hoggart CJ, O'Reilly PF, Whittaker JC, De Iorio M, Balding DJ, Fregene: simulation of realistic sequence-level data in populations and ascertained samples., BMC Bioinformatics, 09-08-2008 [ Abstract, cited in PMC ] |
GSR Certification | ✔ Accessibility |
Last evaluated | 05-03-2018 (2151 days ago) |
Attribute Category | Attribute |
---|---|
Target | |
Type of Simulated Data | Diploid DNA Sequence, Haploid DNA Sequence, |
Variations | Biallelic Marker, Single Nucleotide Variation, |
Simulation Method | Forward-time, |
Input | |
Data Type | |
File format | XML, |
Output | |
Data Type | Genotype or Sequence, Demographic, Mutation, Diversity Measures, |
Sequencing Reads | |
File Format | Other, |
Sample Type | Random or Independent, Case-control, |
Phenotype | |
Trait Type | |
Determinants | |
Evolutionary Features | |
Demographic | |
Population Size Changes | Constant Size, Exponential Growth or Decline, User Defined, |
Gene Flow | Island Models, User-defined Matrix, |
Spatiality | |
Life Cycle | Discrete Generation Model, |
Mating System | |
Fecundity | |
Natural Selection | |
Determinant | Single-locus, Multi-locus, |
Models | Balancing Selection, Multi-locus models, Random Fitness Effects, |
Recombination | Uniform, Varying Recombination Rates, Gene Conversion Allowed, |
Mutation Models | Two-allele Mutation Model (Symmetric), |
Events Allowed | |
Other | |
Interface | Command-line, |
Development | |
Tested Platforms | Mac OS X, Linux and Unix, Solaris, |
Language | C or C++, |
License | GNU Public License, |
GSR Certification | Accessibility, Documentation, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 10
The following 10 publications are selected examples of applications that used FREGENE.
2013
Cule E, De Iorio M, Ridge regression in prediction problems: automatic choice of the ridge parameter., Genet Epidemiol, 11-01-2013 [Abstract]
2012
Bouaziz M, Paccard C, Guedj M, Ambroise C, SHIPS: Spectral Hierarchical clustering for the Inference of Population Structure in genetic studies., PLoS One, 01-01-2012 [Abstract]
2011
Keller MC, Visscher PM, Goddard ME, Quantification of inbreeding due to distant ancestors and its detection using dense single nucleotide polymorphism data., Genetics, 09-01-2011 [Abstract]
Cule E, Vineis P, De Iorio M, Significance testing in ridge regression for genetic data., BMC Bioinformatics, 09-19-2011 [Abstract]
Howrigan DP, Simonson MA, Keller MC, Detecting autozygosity through runs of homozygosity: a comparison of three autozygosity detection algorithms., BMC Genomics, 09-23-2011 [Abstract]
Lipman PJ, Yip WK, AlChawa T, Ludwig KU, Mangold E, Lange C, On the analysis of sequence data: testing for disease susceptibility loci using patterns of linkage disequilibrium., Genet Epidemiol, 12-01-2011 [Abstract]
Bouaziz M, Ambroise C, Guedj M, Accounting for population stratification in practice: a comparison of the main strategies dedicated to genome-wide association studies., PLoS One, 01-01-2011 [Abstract]
2010
Enard D, Depaulis F, Roest Crollius H, Human and non-human primate genomes share hotspots of positive selection., PLoS Genet, 02-05-2010 [Abstract]
Powell JE, Visscher PM, Goddard ME, Reconciling the analysis of IBD and IBS in complex trait studies., Nat Rev Genet, 11-01-2010 [Abstract]
Ayers KL, Cordell HJ, SNP selection in genome-wide and candidate gene studies via penalized logistic regression., Genet Epidemiol, 12-01-2010 [Abstract]