Spatial analysis method (sam): a software tool combining molecular and environmental data to identify candidate loci for selection



    1. Istituto di Zootecnica, Università Cattolica del S.Cuore, via E. Parmense 84, 29100 Piacenza, Italy,
    2. MicroGIS Foundation for Spatial Analysis (MFSA), La Frasse, 1618 Châtel-Saint-Denis, Switzerland,
    Search for more papers by this author

    1. Laboratoire de Systèmes d’Information Géographique, Ecole Polytechnique Fédérale de Lausanne (EPFL), Bâtiment GC, Station 18, 1015 Lausanne, Switzerland,
    Search for more papers by this author

    1. Laboratoire d’Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, BP 53, 38041 Grenoble cedex 09, France
    Search for more papers by this author

Dr Stéphane Joost, Fax: +41 21 691 77 86; E-mail:


sam is a Windows program designed to detect candidate loci for selection in whole-genome scans. It also gives valuable clues as regards the ecological factors at stake in the selection process. The method used is based on multiple univariate logistic regression models to test for association between allelic frequencies at marker loci and environmental variables. The software reads matrices constituted of presence/absence of molecular markers, and of the corresponding environmental parameters at sampling locations. It provides dynamic analysis tables to process the results. The tool is freely available for download at