We present the tool
that simulates genomic inversions in bacterial chromosomes. The tool simulates symmetric inversions but allows the appearance of nonsymmetric inversions by simulating small syntenic blocks frequently observed on bacterial genome comparisons. We evaluate
by comparing its results to real genome alignments. We develop measures that allow quantitative comparisons between real pairwise alignments (in terms of dotplots) and simulated ones. These measures allow an evaluation of
in terms of dendrograms. We evaluate
by comparing its results to whole chromosome alignments and maximum likelihood trees for three bacterial groups (the
family and the
genera). We demonstrate an application of
by using it to evaluate the ancestral genome reconstruction tool MGR.