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LOGICIELS

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

 

  • BayeScan (BAYEsian genome SCAN for outliers).
    A free software that identifies outlier loci. It's applicable to both, dominant and codominant data.  
    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).

 

  • BIMr  (Bayesian Inference of imMigration rates. A new Bayesian method to identify the environmental factors that influence recent migration).

    Pierre Faubet (pierre.faubet@e.ujf-grenoble.fr)
    and Oscar Gaggiotti (oscar.gaggiotti@ujf-grenoble.fr).

    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.
    BIMr is distributed under the terms of the GNU General Public Licence (GPL) and is available for all three major platorms. Corresponding instructions are given in the manual.
    Below are examples of input files :

    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.).
     

    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. It was developped by Alain Cercueil, O. François and S. Manel. 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.

 

  • GESTE    (GEnetic STructure inference based on genetic and Environmental data) 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.).

    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.

 

 

  • scanAFLP v1.0  
    scanAFLP implements a semi-automatic and repeatable method to score data for dominant molecular markers (e.g. AFLPs). scanAFLP is a user-friendly script written and working in an R environment. This R script interprets PCR product fluorescence (fragment size and fragment height) data matrices created by softwares such as Applied Biosystems’ GeneMapper and converts them into presence-absence (1-0) phenotype tables according to quality and repeatability criteria.

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

 

  • 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    [documentation pdf].

    • WOMBSOFT windows.                      WOMBSOFT linux et Mac.

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