Genepop reference page
Genepop is now distributed both as an R package on CRAN, and as a stand-alone executable on this page. Both are based on the the latest version of the Genepop C++ sources, currently version 4.7.5 (23 February 2020; Rousset, 2008).
Also available here is a recompiled version of the linkdos program (Garnier-Géré and Dillmann 1992), which was distributed with previous versions of Genepop. Linkdos is not part of Genepop itself.Full version 4.7 distribution: download GenepopV4.tar.gz or GenepopV4.zip.
Documentation: download Genepop4.7.pdf
Version 4.7 Windows
Executables (32 and 64-bit versions): download exe.zip (checked with virustotal
on 2020/02/24).
Example files: download examples.zip.
Version 4.7 sources (Windows, Linux, Macintosh; also linkdos source): download sources.tar.gz or sources.zip
Macintosh users (OS X): recompile the sources as for Linux.
In case of problem with files obtained from this page, please report to me (not to Eleanor Morgan); and read the documentation first.
Genepop 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 also covered by a GPL-compatible licence (in particular, with freely available source code, even if commercial software), and provided the Genepop source is acknowledged (of course... well, that does not seem obvious to everyone. See the GPL!).
See the documentation for all further information.
© François Rousset 2007-now
See the NEWS
of the R package for changes from version 4.7.0 onwards.
What was new to version 4.6?
A bootstrap analysis of mean differentiation has been introduced, in particular to allow comparison of differentiation over a given range of geographical distances, in intra vs. inter-ecotypic analyses. In can be called by the setting meanDifferentiationTest. The Mantel test based on regression slope (not the one on ranks) was not handling appropriately cases where some pairwise data had to be excluded (thanks again to T. de Meeus for pointing this). This iscorrected.
What was new to version 4.5.1?
A bug was found and corrected in the Mantel test when performed after a bootstrap (thanks to Thierry de Meeus for spotting discrepancies between Mantel tests).
What was new to version 4.5?
A new keyword inter_all_pairs for setting "popTypeSelection" allows one to perform spatial regressions (but not Mantel tests) between all pairs of individuals or populations belonging to different types (e.g., individuals belonging to different patches, excluding pairwise statistics for pairs of individuals within patches). The inter-OS input file checks have been modfied (again), to address a persistent problem on Mac OS X.
What was new to version 4.4?
Mantel tests are by default no longer based on rank correlation of the distances, but instead on the correlation of the distances. The older rank tests can be performed using the new MantelRankTest setting. In addition, a MaximalDistance setting has been added, affecting the computation of spatial regressions in a way similar to MimimalDistance (but this new setting is best ignored in normal use).
What was new to version 4.3?
New options 8.5 to retain individual names when converting population data to individual data, and 8.6 for generation of haploid genotypes by random sampling in diploid genotypes. Much code tidying to avoid warnings with stricter compilers than vanilla g++..
Older changes since version 4.0.5.3 (first advertised release of fully rewritten Genepop):
4.2.2: Only a cryptic
bug fix which won't change any Genepop output, and more
changes to comply with the clang compiler
stricter syntax checks. 4.2.1: More cryptic
changes in input file checks (again).
4.2: One can perform all isolation-by-distance
analyses with a user-provided distance matrix. Cryptic
changes in inter-OS input file checks (again) and in
the way locus names are read, which could previously
make Genepop crash.
4.1.4: Wrong files were included in
version 4.1.3. This new release corrects for this. 4.1.3:
This version
intended to correct two problems with the IsolationFile
option: the source file was not correctly read and (for
Windows only) the results when not correctly
displayed. 4.1.2: The Windows executables
included in version 4.1.1 were not portable and this is
corrected. The genotypic disequilibrium test treated
incomplete genotypes as full genotypes and this is
corrected. 4.1.1: Again
some cryptic changes in inter-OS input file checks;
correction of a crashing bug for a missing-data case
in LD testing; but nothing really new in the
code. 64-bit executables for
Windows. (but see version 4.1.2)
The LINKDOS.exe which was missing from the v.4.1
distribution, has been restored.
4.1: (1) It is possible to test trends in gene
diversity among samples. (2) Analyses of isolation by distance have
been strengthened in several ways. Variants of
previously described estimators have been implemented
for both haploid and diploid data. 0ne can select
subsets of the data for analyses of isolation by
distance within and between these subsets. Further,
analysis of isolation by distance from several one-locus
genetic distance matrices is now possible through the
MultiMigFile option. In contrast to IsolationFile, this
allows the construction of bootstrap confidence
intervals. Finally, it is possible to test specific
values of the slope of the spatial regression, using the
testPoint setting. (3) The input file
reading procedure is better protected against nonstandard
file formats (in particular those produced by some
Microsoft software under Mac OS X). (4) The new
sub-option 8.4 has been added to convert population-based
data to individual-based data (each individual in its own
Pop). v.
4.0.6 (05/09/2007): corrected
a change in v. 4.0.5.3 which made settings files
unreadable under Windows. Sample
file sampleSettings.txt also corrected to match the
examples in the Documentation. v. 4.0.7 (25/11/2007): corrected a bug in the Mantel test when
some samples had null geographic distance. v. 4.0.8 (28/01/2009): corrected a minor file reading bug in
linkage disequilibrium test when pop strings were
followed by tab characters. v.
4.0.9 (02/03/2009): can
now convert 3-digits data to Linkdos format. v. 4.0.10 (28/04/2009): cosmetic changes + updating #include's
for compilation with g++ 4.3.2. v. 4.0.11 (25/06/2010): corrected a bug (introduced in version 4)
for computation of P-values from chi2 distribution with
large df's. Also some more cryptic changes including new
procedures for checking input file format, in principle
less dependent on operating system distribution-specific
features.