SNeP: A tool to estimate trends in recent effective population size trajectories using genome-wide SNP data

Mario Barbato*, Pablo Orozco-Terwengel, Miika Tapio, Michael W. Bruford

*Autore corrispondente per questo lavoro

Risultato della ricerca: Contributo in rivistaArticolo in rivista

142 Citazioni (Scopus)


Effective population size (N<inf>e</inf>) is a key population genetic parameter that describes the amount of genetic drift in a population. Estimating N<inf>e</inf> has been subject to much research over the last 80 years. Methods to estimate N<inf>e</inf> from linkage disequilibrium (LD) were developed ~40 years ago but depend on the availability of large amounts of genetic marker data that only the most recent advances in DNA technology have made available. Here we introduce SNeP, a multithreaded tool to perform the estimate of N<inf>e</inf> using LD using the standard PLINK input file format (.ped files) or by using LD values calculated using other software. Through SNeP the user can apply several corrections to take account of sample size, mutation, phasing, and recombination rate. Each variable involved in the computation such as the binning parameters or the chromosomes to include in the analysis can be modified. When applied to published datasets, SNeP produced results closely comparable with those obtained in the original studies. The use of SNeP to estimate Ne trends can improve understanding of population demography in the recent past, provided a sufficient number of SNPs and their physical position in the genome are available. Binaries for the most common operating systems are available at
Lingua originaleEnglish
pagine (da-a)1-6
Numero di pagine6
RivistaFrontiers in Genetics
Stato di pubblicazionePubblicato - 2015


  • Demography
  • Effective population size
  • Genetics
  • Genetics (clinical)
  • Large scale genotyping
  • Linkage disequilibrium
  • Molecular Medicine
  • SNPChip


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