Representations of a comparison between the human and the mouse X chromosomes, produced from the same input data by PhylDiag (A) and i-ADHoRe 3.0.2a (B). The maximum gap parameter g a p
is equal to 5 and the merging process used the DPD metric in both cases. In figure A each axis displays explicitly the paths to the files containing the relevant genome data, the name of the chromosome and the chromosomal window range. As in ADHoRe sbs identified by PhylDiag are surrounded by a rectangle and each sb is drawn in a specific colour. In figure B blue dots represent a confidence interval around each sb drawn in yellow. The long synteny block in the middle of the ADHoRe MHP is in two parts in the PhylDiag MHP because the two extremities are spaced by a distance higher than 5 using the DPD metric. By default ADHoRe has a special feature using extremities of diagonals during its merging process, however this feature cannot be deactivated which may lead to undesired merges.