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genepopedit specifications


Unique identifier OMICS_20127
Name genepopedit
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
dplyr, data.table, reshape2, stringr
Maintained Yes




No version available



  • person_outline Brendan Wringe
  • person_outline Ryan Stanley
  • person_outline Ian Bradbury
  • person_outline Nick Jeffery

Publication for genepopedit

genepopedit citations


Range wide parallel climate associated genomic clines in Atlantic salmon

R Soc Open Sci
PMCID: 5717698
PMID: 29291123
DOI: 10.1098/rsos.171394
call_split See protocol

[…] ed SNPs missing data in greater than 15% of individuals and removed these. We filtered the North American and European datasets to 1773 loci common to all locations and SNP arrays using the R package genepopedit []. While we note that our European data are unbalanced due to the inclusion of a high density of northern English and Scottish rivers, we investigated whether random subsetting these rive […]


Applications of random forest feature selection for fine‐scale genetic population assignment

Evol Appl
PMCID: 5775496
PMID: 29387152
DOI: 10.1111/eva.12524

[…] rameters set to default.We further reduced our panel for downstream feature selection by removing redundant SNPs and SNPs in linkage disequilibrium using the genepop_toploci function in the R package Genepopedit (Stanley, Jeffery, Wringe, DiBacco, & Bradbury, ) at an R 2 threshold of 0.2 and a minimum global F ST of 0.05. Although this is a highly stringent approach, reductions in the data set are […]


RAD sequencing reveals genomewide divergence between independent invasions of the European green crab (Carcinus maenas) in the Northwest Atlantic

Ecol Evol
PMCID: 5395438
PMID: 28428843
DOI: 10.1002/ece3.2872
call_split See protocol

[…] ne SNP per RAD tag was retained to remove the effects of physical linkage. The resulting panel was converted for subsequent analyses using PGDSpider v2.0.8.3 (Lischer & Excoffier, ) and the R package genepopedit (Stanley, Jeffery, Wringe, DiBacco, & Bradbury, 2017). […]


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genepopedit institution(s)
Bedford Institute of Oceanography, Dartmouth, NS, Canada; Department of Computer Science, Dalhousie University, Halifax, NS, Canada; Northwest Atlantic Fisheries Science Centre, St. John’s, NL, Canada
genepopedit funding source(s)
Funding for this work has been provided through the NSERC Canadian Healthy Oceans Network (CHONe) and the Genomics Research and Development Initiative of Fisheries and Oceans Canada.

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