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 0.5): Migraine now includes a new model, OnePopFounderFlush, and a resampling procedure improving the importance sampling algorithm in the OnePopVarSize model. Further, it now uses a standard R package, blackbox, rather than the older Rmigraine package that was previously distributed through this page, so that installation is easier.

Older changes: Version 0.4.1 corrected a major bug introduced for isolation by distance in the previous update (, Feb 20)

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 (Leblois et al., 2014) or an ISM; 
  • the OnePopFounderFlush model.

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.

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

For the sources for all operating systems, download migraine.tar.gz.

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 (C) François Rousset & Raphaël Leblois 2007-present, with additional contributions by Champak R.Beeravolu 2013-2014.

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.

This page (C) F. Rousset 2007-present

Source/executables last updated on 2016/09/02

Documentation last updated on 2016/09/02

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