Aligning divergent mitochondrial genomes - software recommendations?

Question

[ryan.gawryluk]

Hello,

I am trying to align mitochondrial genomes from a few completely novel protists. Although I can see from the mitochondrial genome maps that there is conserved gene content and fairly large syntenic regions, I am unable to visualize the synteny with Mauve, because it is poorly suited to comparing genomes that are dissimilar at the nucleotide level.

I am looking for recommendations of genome alignment software that might have been developed for comparing more divergent (small) genomes, for instance by taking the translated ORFs into consideration when doing alignments.

Thanks for any recommendations!

Ryan