Population genomics

A free software that estimates F-statistics using dominant data. The method implemented in ABC4F corrects for the ascertainment biases that characterise AFLP markers.

Download :

– Windows binary : ABC4F.zip
– Source code : ABC4F_src.zip

This program is distributed under the terms of the GNU General Public Licence (GPL).

The method is described in the following publication :
Foll, M, M.A. Baumont and O.E. Gaggiotti, 2008. An Approximate Bayesian Computation approach to overcome biases that arise when using AFLP markers to study population structure.Genetics, 179:927-939.
 

A free software that identifies outlier loci. It’s applicable to both, dominant and codominant data.

– Downloads ands informations on BayeScan website

This program is distributed under the terms of the GNU General Public Licence (GPL).

The method is described in the following publication :
Foll, M and O.E. Gaggiotti, 2008. A genome-scan method to identify selected loci appropriate for both dominant and codominant markers : A Bayesian perspective. Genetics, (in press).
 

A new Bayesian method to identify the environmental factors that influence recent migration. BIMr is a free software that makes inferences about recent proportions of immigrant genes in subdivided populations and that identifies the environmental factors that are responsible for observed gene flow patterns.

Download :

– Linux binary : BIMr-linux-i686.tar.gz
– Mac OS X binary : BIMr.dmg
– Windows binary : BIMr.zip
– Source code : BIMr-src.tar.gz

Corresponding instructions are given in the manual.

This program is distributed under the terms of the GNU General Public Licence (GPL). It is available for all three major platorms.

Contacts : Pierre Faubet and Oscar Gaggiotti

The method is described in the following publication :
Faubet P. and O.E. Gaggiotti, 2008. A new Bayesian method to identify the environmental factors that influence recent migration. Genetics 178 : 1491–1504.
 

COLONISE is a user-friendly Microsoft® Windows software for the study of colonisation events in natural populations. It determines the composition of the newly colonised population and makes inferences about the factors that influenced individuals to establish a new population. COLONISE uses a hierarchical Bayesian model to combine multilocus genotype data with demographic and environmental data, and a reversible jump MCMC algorithm to perform posterior density estimations. The software is written in C and C++ for the graphical user interface. It integrates a tool to draw posterior density functions (histogram, running mean, traces, etc.) and to estimate parameters from them (mean, mode, variance, HPDI etc.)

Download :

– Windows binary : Colonise.zip

This program is distributed under the terms of the GNU General Public Licence (GPL).

The method is described in detail in the following publication :
Gaggiotti, O. E., S. P. Brooks, W. Amos and J. Harwood, 2004 Combining demographic, environmental and genetic data to test hypotheses about colonization events in metapopulations. Molecular Ecology 13 : 811-825.

The software is described in the following computer note :
Foll, M., and O. E. Gaggiotti, 2005 COLONISE : a computer program to study colonization processes in metapopulations. Molecular Ecology Notes 5 : 705-707.
 

GENBMAP is a user-friendly Microsoft® Windows software for the study of the spatial genetic structure. The method is essentially descriptive, and allows an user to analyze genotypes and geographic coordinates simultaneously through a two dimensional graphical representation. GenBMAP provides a basis for the interpretation of the genetic structure of a population.

Contacts : Alain Cercueil, O. François and S. Manel.
 

GESTE is a Bayesian method to evaluate the effect that biotic and abiotic environmental factors (geographic distance, language, temperature, altitude, local population sizes, etc.) have on the genetic structure of populations. It can also be used to study spatial population processes, such as range expansions, by simply introducing longitude and latitude as the explanatory variables.

GESTE estimates FST values for each local population and relates them to environmental factors using a generalized linear model. The method requires genetic data from codominant markers (e.g. allozymes, microsatellites, or SNPs) and environmental data specific to each local population. The software is written in C++ and integrates a tool to draw posterior density functions (histogram, running mean, traces, etc.) and to estimate parameters from them (mean, mode, variance, HPDI etc.).

Download :

– Windows binary : GESTEv2.zip

This program is distributed under the terms of the GNU General Public Licence (GPL).

The method is described in the following article :
Foll, M., and O.E. Gaggiotti, 2006. Identifying the environmental factors that determine the genetic structure of Populations. Genetics 174 : 875-891.
 

ISIF (In SIlico Fingerprinting) : A free user-friendly software that performs in silico AFLP (can also be applied for DART or RAD).

Download :

– isif.exe.zip

The program runs under windows and needs the Microsoft .NET Framework version 2.0 (freely available here).

The method and validation of the program is described in the following article :
Paris, M., Bonnes, B., Ficetola, G.F., Poncet, B.N., Despres, L. (2010) Amplified fragment length homoplasy : in silico analysis for model and non-model species. BMC Genomics 11:287.

The manual of utilisation is described in the following chapter :
Paris, M., Despres, L. (2012) In Silico Fingerprinting (ISIF) : A User-Friendly In Silico AFLP Program. In "Data Production and Analysis in Population Genomics" (Bonin A, Pompanon F eds). Methods in Molecular Biology Series, Humana Press. 888:55-64.
ISIF (.exe)
 

Computer program for parentage analysis (2002) Cercueil Alain, Eva Bellemain and Stéphanie Manel, Journal of Heredity, 93 : 458-459).

Download :

– Parente.zip

Contacts : Eva Bellemain and Alain Cercueil
 

A R script to evaluate AFLP electropherograms for phenotyping and marker selection based on peak height distribution and repeatability using blind controls.

Download :

– ScanAFLP.zip

The method is described in the following publication :
Herrmann D., Poncet B. N., Manel S., Rioux D., Gielly L., Taberlet P., Gugerli F (2010) Selection criteria for scoring amplified fragment length polymorphisms (AFLPs) positively affect the reliability of population genetic parameter estimates. Molecular Ecology 53:302-310.
 

WOMBSOFT is a collection of R functions Wombling-based that analyse individually geo-referenced multilocus genotypes for the inferences of genetic boundaries between populations. The software produces two maps. The first shows the variations in systemic function and the variations in the mean direction of the gradient in the studied area. The second map represents candidate boundary elements that are significant at the chosen level. It can be used with codominant or dominant markers.

Downlaod :

– WOMBSOFT windows
– WOMBSOFT linux et Mac
– Documentation pdf