Compare mus musculus and mus spretus genome structure annotation

Question

[arta]

I would like to compare genome structure (gene models) annotation of Mus Musculus and Mus Spretus in terms of gene order, chromosome location etc... . So at the end i would like to come up how similar they are. I have both gtf files from Ensemble.

I have checked that link, but most of the links are death and old. Some tools or packages might have been published for the last 7 years ?

Thanks for the help.

[kashiff007]

You can use any annotation comparison tools. I found MCScanX. more useful. Along with the homologs (both paralogs and orthologs) it alos determines duplicates, tandem repeats, collinearity, gene family tree and few more.

It can also calculate the ka ks value using which you can track time of speciation of these two species.