invertFREGENE protocols

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invertFREGENE specifications

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Unique identifier OMICS_15329
Name invertFREGENE
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format XML
Output format TXT
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Source code URL https://www.ebi.ac.uk/sites/ebi.ac.uk/files/groups/kersey_service_team/FREGEN/invertfregene.tar.gz
Maintained Yes

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  • person_outline Clive Hoggart <>

invertFREGENE in pipeline

2015
PMCID: 4700947
PMID: 26560338
DOI: 10.1093/gbe/evv214

[…] h1 homozygous samples (n = 150) (supplementary table s1, supplementary material online). to assess the statistical significance of tajima’s d, genetic data were then simulated under neutrality using invertfregene software () for a total of 1,000 runs. as an overview, the simulation framework begins with the introduction of a 500-kb inversion in a panmictic population of constant size (ne = […]


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invertFREGENE in publications

 (3)
PMCID: 4700947
PMID: 26560338
DOI: 10.1093/gbe/evv214

[…] h1 homozygous samples (n = 150) (supplementary table s1, supplementary material online). to assess the statistical significance of tajima’s d, genetic data were then simulated under neutrality using invertfregene software () for a total of 1,000 runs. as an overview, the simulation framework begins with the introduction of a 500-kb inversion in a panmictic population of constant size (ne = […]

PMCID: 3392271
PMID: 22808122
DOI: 10.1371/journal.pone.0040224

[…] inversion polymorphisms (see methods)., we estimated the power of our method to detect inversions from snp genotype data using simulated inversions generated by recently developed software, invertfregene . for the simulating parameters, such as rates of recombination and mutations, we used the values tested in . we simulated inversions of varying lengths (from 100 kb to 2 mb) and two […]

PMCID: 3296650
PMID: 22321652
DOI: 10.1186/1471-2105-13-28

[…] methods by constructing "artificial" inversions by reversing the order of snps in phased haplotypes from hapmap. we provide a more rigorous test of our method by employing a recent software tool, invertfregene [], that utilizes coalescent theory and suppression of recombination between inverted and normal chromosomes to produce artificial haplotype and genotype data. lastly, we apply […]


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