Migraine distribution page



Migraine implements coalescent algorithms for maximum likelihood analysis of population genetic data. The data currently  handled are allelic counts but sequences will be handled in the forthcoming version. The code is designed to be compiled with the GNU C++ compiler under Windows and Linux (including its Mac OSX incarnation).

Recent changes: Version 0.4.0.1 has been released on 2014/02/20

The latest version includes the OnePopVarSize model, a model of variable population size for a single population; and it can fit data under a generalized stepwise mutmation model (GSM) for this demographic scenario. Thus the different models that can be fit are

  • one- and two-dimensional isolation by distance models (including the island model as a subcase) (Rousset and Leblois 2007,2012);
  • the two-populations model described in de Iorio et al. (2005);
  • the elementary one-population model (with 2Nμ as unique parameter);
  • the OnePopVarSize model, including markers evolving under a GSM (ms under review). 

Typical analyses can be performed in seconds (in the one-parameter case) or overnight (in some three-parameter cases), and longer analyses can easily been split among different computers.

There are two versions of the documentation, a short one that should be sufficient for most applications, and a longer one for complications, which hopefully no one needs to read.

The distribution includes an R package (Rmigraine). 

For Windows executable (migraine.exe) in 32- or 64-bit environments, download either migraineWin32.tar.gz or migraineWin64.tar.gz.

For the sources (migraine and Rmigraine) for all operating systems, download migraine.tar.gz and the Rmigraine_0.3-4.tar.gz package sources.

For the "first session" sample files, download examples.zip.

Current developments: models of variable population size and of population divergence; infinite site model and SNPs.

See the documentation for all further information.


Migraine is freeware (i.e. you don't need to pay). It is free software covered by the CeCILL licence (GPL compatible), i.e. it can be used, copied, studied, modified, and redistributed in other free software (i.e. also covered by a GPL-compatible licence, with freely available source code, even if commercial software) provided the Migraine source is acknowledged.

Funding: Migraine development has benefitted from ANR grants and is currently hosted within the IBC

Migraine (C) François Rousset (CNRS & University Montpellier 2) & Raphaël Leblois (INRA) 2007-present, with additional contributions by Champak R.Beeravolu (postdoc INRA) 2013-present.

This page (C) F. Rousset 2007-present

Source/executables last updated on 2014/02/20

Documentation last updated on 2013/12/20

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