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LOGICIELS
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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.
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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.
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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.
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ISIF (In SIlico
Fingerprinting) :
A free user-friendly software that performs in silico AFLP (can also be applied for DART or RAD).
The program runs under windows and needs the Microsoft .NET Framework version 2.0
(freely available at http://www.microsoft.com/downloads ).
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)
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PARENTE : computer
program for parentage analysis (2002) Cercueil Alain, Eva Bellemain and Stéphanie Manel, Journal of
Heredity, 93: 458-459).
Eva Bellemain (eva.bellemain@ujf-grenoble.fr)
et Alain Cercueil (alain.cercueil@imag.fr) sont deux
étudiants en thèse du LECA.
Parente.zip (Le fichier parente.zip contient tous les fichiers nécessaires pour l'utilisation du logiciel).
- ScanAFLP : a R
script to evaluate AFLP electropherograms for phenotyping and marker selection based on peak
height distribution and repeatability using blind controls.
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.
Zip File
- 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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