I would like to sorted scaffolds of a draft genome according to a reference genome. I used Mauve program. It reordered, but when I checked order of scaffolds of the draft genome, it seems that Mauve did not reorder scaffolds of the draft genome.
For instance, in first analysis (alignment of the genomes) scaffold 1 of the reference genome matched with scaffold 116 of the draft. When I reordered, the scaffold 116 did not replaced as the first scaffold of the reference genome.
I am using a worm species genomes for reordering.