How best to decrease computation time?

[RvV1979]

Thanks for developing such a versatile tool; especially the ability to integrate annotations is very nice. However, I find that running comparisons of relatively long sequences is prohibitive.
Specifically, I started an all-vs-all comparison of three plant genome sequences of 0.9, 2.7, and 5.6 Mb and it is still running after almost one day. Below are the settings used:
flexidot_v1.06.py -i JAATIP010000026.1.fas,JAATIP010000103.1.fas,UZAU01000736.fas -k 70 -p 2 -f 2 -w 0 -L 1 -g genes.gff -G gff_color.config
Are such runtimes expected for such sequence lengths, and if so, do you have any recommendations for speeding things up?

Thanks