Introduction

CARTHAGENE is a computer tool for building genetic and/or radiated hybrid maps. For those who don't know, radiation hybrid mapping is a somatic cell technique which is used for ordering markers and estimating a physical distances between them (chromosomes are broken by irradiation) expressed in centiRay (instead of centiMorgan).

The main specificity of CARTHAGENE lies in the fact that it can build maximum likelihood ``consensus'' maps for several data sets corresponding to different populations but it can naturally also handle single population mapping.

The main strengths of CARTHAGENE can be rapidly described as follows:

• it can merge data sets from several types, both genetic and radiated hybrid data, assuming either shared ``distances'' or not between different populations.
• it always uses maximum multipoint likelihood as the criterion to compare maps, a rigorous well-behaved criterion. With optimized algorithms for backcross and haploid RH data, CARTHAGENE can, with no loss of precision, be one or two order of magnitude faster than alternative algorithms using the same criterion.
• it contains several powerful algorithm for building and validating both comprehensive and framework maps.
• it does not simply return a supposedly optimal map but a set of the $k$ best maps that have been encountered during search. This gives feedback on the reliability of a map ordering.
• it has a graphical interface where maps can be visualised and compared and a text interface with an underlying programming langage (called Tcl) which can be used to automate mapping. If you intend to develop automated mapping procedure, you can get more documentation on the Tcl langage at http://www.tcl.tk/doc/. If you prefer, a Perl interface has also been independently developped by W.M. Snelling (USDA).
• it can be used on several plateforms (unix, Linux, Windows).

This document is the user guide of CARTHAGENE. It is intended for any user that would like to use CARTHAGENE. It essentially describes the textual interface of CARTHAGENE where commands are issued, the graphical interface is considered to be intuitive enough to be understandable once the textual interface is mastered.

For installing CARTHAGENE on your system, please go to CARTHAGENE's home page on the web:

http://www.inra.fr/bia/T/CarthaGene.