Analysing multilocus population data.

Platforms & distributions

  • platform-independent source code
  • posix


Development status


Latest version

See below.


This program has been written to facilitate analysis of multi-locus population genetic data. In particular, it allows calculation of various genotypic diversity indices, various linkage disequilibrium indices, and a measure of population differentiation, and allows one to search for subpopulations which do not share polymorphisms (and thus might be reproductively isolated). It includes a modification of the IA (Index of Association) metric that corrects the scaling effect seen when one applies the metric to different numbers of loci. In addition, there are randomization routines which allow one to test various null hypotheses.

If this software is used in any publication, cite:

Agapow & Burt (2001) “Indices of multilocus linkage disequilibrium”, Molecular Ecology Notes 1, pp101-102.

Due to life and career changes, enquiries about technical matters and the future of Multilocus should be directed to Austin Burt.


Precompiled binaries are available for several platforms. It can also be compiled from source. In a unix-like environment (Linux, OSX, etc.), this can be done with the usual unix incantations:

# unpack the archive
% tar zxvf multilocus-1.3.tgz
# change into the archive
% cd multilocus-1.3
# configure
% ./configure
# compile
% make

The compiled executable can now be moved to any useful location.

The code can probably be compiled in other environments using other compilers. I cannot help you with this.


A full manual is included in the distribution.


Pay attention to the input formats defined in the manual. Input files are plaintext files not Word or Excel documents.


  • Agapow & Burt (2001) “Indices of multilocus linkage disequilibrium”, Molecular Ecology Notes 1, pp101-102