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Bioinformatics Advance Access published online on December 14, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti222
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Bioinformatics © Oxford University Press 2004; all rights reserved.
Received September 14, 2004
Revised November 3, 2004
Accepted November 3, 2004

Applications note

CARHTAGENE: multipopulation integrated genetic and radiated hybrid mapping

Simon de Givry 1*, Martin Bouchez 1, Patrick Chabrier 1, Denis Milan 1, and Thomas Schiex 1

1 INRA, Biométrie et Intelligence Artificielle/Génétique Cellulaire, BP 27, 31326 Castanet-Tolosan Cedex, FRANCE

* To whom correspondence should be addressed.
Simon de Givry, E-mail: carthagene{at}ossau.toulouse.inra.fr


  Abstract

Summary: CARHTAGENE is an integrated genetic and radiated hybrid mapping tool which can deal with multiple populations, including mixtures of genetic and RH data. CARHTAGENE performs multipoint maximum likelihood estimations with accelerated EM algorithms for some pedigrees and has sophisticated algorithms for marker ordering. Dedicated heuristics for framework mapping are also included.

CARHTAGENE can be used as a C++ library, through a shell command and through a graphical interface. XML output for companion tools is integrated.

Availability: The program is available free of charge on www.inra.fr/bia/T/CarthaGene for Linux, Windows and Solaris machines (with Open Source).


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