ProCars is a program used to reconstruct Ancestral gene orders as CARs (Contiguous Ancestral Regions) with a progressive homology-based method. The method runs from a phylogeny tree (without branch lengths needed) with a marked ancestor and a block file.
This homology-based method is based on iteratively detecting and assembling ancestral adjacencies, while allowing some micro-rearrangements of synteny blocks at the extremities of the progressively assembled CARs.
The method starts with a set of blocks as the initial set of CARs, and detects iteratively the potential ancestral adjacencies between extremities of CARs, while building up the CARs progressively by adding, at each step, new non-conflicting adjacencies that induce the less homoplasy phenomenon. The species tree is used, in some additional internal steps, to compute a score for the remaining conflicting adjacencies, and to detect other reliable adjacencies, in order to reach completely assembled ancestral genomes.