Variation of Effective size


  • N.Nikolic, LGC, INRA, Toulouse, France (contact author)
  • C.Chevalet , LGC, INRA, Toulouse, France


This package estimates the effective sizes from actual to ancestral time with a coalescent approach. It works on steps of constant size to resolve the probabilities by an approximation of maximum likelihood from a Bayesian posterior distribution.

Citing Articles:
-Nikolic N, Chevalet C 2014. Detecting past changes of effective population size. Evolutionary Applications. DOI: 10.1111/eva.12170
-Chevalet C & Nikolic N. 2010. Distribution of coalescent times and distances between microsatellite alleles with changing effective population size. Theoretical Population Biology. Volume 77, Issue 3: 152-163


Software VAREFF (package R in and the documentation

This package works with R software version 3.0.2 or later for VAREFF version 1.1 and R software version 2.10.0 or later for VAREFF version 1.0.


This new version contains a new function TMRCA to estimate the time of the detected bottleneck.
Dowload Manual V.1.2
Dowload the PDF Help V.1.2

Dowload Manual V.1.0
Dowload the PDF Help V.1.0

Program to built the INFILE

To convert genotype file to VarEff file use the Excel Macro

To convert an MSVAR file in VarEff file by using the Excel Macro

To convert data file formats between VarEff and MSVAR by using R script VarEffMSVAR (read the Chapter G in SUMMARY)


New Fonction to complement VarEff Results and estimate the likelihood frequency of a bottleneck detected : Function BTlike

Dowload R.source here
Dowload the Help file here