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 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
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: