How to measure the robustness of bacterial genome comparisons?

The number of studies dealing with complete bacterial genome comparisons steadily increases. They allow us to gain insight into the molecular mechanisms involved in the evolution of bacterial genomes such as DNA exchanges. There exist several software tools and methods to align complete genomes and to determine conserved and variable regions. However, statistical methods to evaluate these tools are lacking. To fill this gap, two local scores for measuring the robustness of the comparisons of bacterial genomes are proposed. The calculation procedures of these scores are first presented and their interest is then discussed from two illustrative examples