I am trying to reorder scaffolds of a rice species, but no genetic map is available right now. Oryza sativa Japonica is a close relative of this rice species. Mummer was used to do a whole genome alignment, and I am trying to reorder scaffolds according the mummer result. But I found it's too complicated to do this by myself, many scaffolds may align to multiple Oryza sativa Japonica chromosomes or multiple loci in the same chromosome.
What software can I use to handle this task?