The lab I work with would like to compare a few populations' genomes of a species with an unpublished genome assembly. I have sequence data for each population that was created using only single-size insertion sequences, yielding only short paired-end reads. I was able to create a genome assembly for one of the populations and would like to see how it compares to another closely related species (which has a published genome). I used Augustus (http://bioinf.uni-greifswald.de/augustus/) to produce a GFF annotation for my assembly but am not sure how to best go about comparing my assembly to the published assembly of the other species. Can Galaxy help? Are there other tools that may be of use? I tried using ACT (http://www.sanger.ac.uk/resources/software/act/) but it never finished. These genomes are approximately 1Gbp. Any advice would help.