I want to do a complete genome alignment of fungal isolates using the MUMmer software NUCmer and PROmer algorithms
I want to determine the degree of overlap between genomes
how can I do that??
What do you mean by 'overlap'?
How many genomes have you got? if its more than about 4-5, alignment is not the right approach.
Please edit your post with much more information, it's hard to drag it out one word at a time to get to an answer.
I have 10 genomes , I want to make a comparative analysis of these genomes to determine the evolutionary relationship between the strains
You cannot align that many genomes of that size. It simply won't work.
If you want to know similarity, you could use fastANI, or mash sketches. If you want to infer phylogenetic relationships though, you will probably be best off trying to define a core genome, and then using concatenated gene alignments.
my strains have 4 chromosomes, can I compare chrormosome by chromosome or gather all genes (concatenated) in a sequence and deduce it as a single genome
You could probably do either, so long as your orthologue clustering is sufficiently reliable