Reordering scaffolds according to a reference without a genetic map 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?
Have you tried Mauve alignment? Its pretty easy once you become familiar and has a GUI for further ease of use. Additionally there are a few online tutorials on how to re-order contigs/ scaffolds using this software. Heres one I use when in need.

Mauve contains a function called Mauve Contig Mover (MCM) which can be used to a) compare an assembly to a reference and/or b) rearrange contigs to improve assembly quality.   

I use the tutorial as above which uses the GUI for Mauve. I