Building maps from scratch

In CARTHAGENE everything starts by building a first initial map from the current set of selected markers. This first map will be stored in the heap and will be used ad the indispensable ``seed'' for further map improving commands. There are several methods to produce sucha first map and they can be simply classified as methods that aim at providing comprehensive maps and methods that aim at providing framework maps.

• Comprehensive maps are maps that will contain all the markers mentionned in the set of currently active markers. The maps sought are typically maps whose loglikelihood is maximum in this case.
• Framework maps are maps that may contain a subset of the markers mentionned in the set of currently active markers. The aim is to select markers that can be reliably ordered (i.e., which can be ordered in such a way that all alternative orders are less likely by several orders of magnitudes).

All the initial mapping commands of CARTHAGENE are simple heuristics commands that do not spend a large amount of time trying to build an ideal map. The consequence of this, which is true for all existring software using such ``quick'' mapping techniques, is that the maps produced by CARTHAGENE may be still be improved. For this, use the ``improving'' commands (section 2.6).