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Bioinformatics Advance Access originally published online on June 22, 2007
Bioinformatics 2007 23(16):2188-2189; doi:10.1093/bioinformatics/btm315
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

MareyMap: an R-based tool with graphical interface for estimating recombination rates

Clément Rezvoy , Delphine Charif , Laurent Guéguen and Gabriel A.B. Marais *

Université de Lyon; Université Lyon 1; Centre National de la Recherche Scientifique; UMR5558; Laboratoire de Biométrie et Biologie évolutive; Villeurbanne, F-69622 cedex, France

*To whom correspondence should be addressed.


  Abstract

Summary: Comparing genetic and physical maps (the so-called Marey map approach) is still the most widely used approach to estimate genome-wide recombination rates. Remarkably, there is no available bioinformatics tool specifically devoted to Marey map approach. Here, we developed such a tool called MareyMap based on GNU R and Tcl/Tk. MareyMap offers a user-friendly graphical interface and includes useful features, such as data cleaning process, sophisticated interpolation methods to estimate local rates, possibility of complex queries, various range of import–export files. Moreover, MareyMap comes with ready-to-use maps for human, Drosophila, Caenorhabditis elegans and Arabidopsis. MareyMap has been made so that it can be easily upgraded with new data and interpolation methods.

Availability: http://pbil.univ-lyon1.fr/software/mareymap/

Contact: marais{at}biomserv.univ-lyon1.fr

Associate Editor: Keith Crandall

Received on March 6, 2007; revised on May 14, 2007; accepted on June 6, 2007

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