how can I do a genome comparative analysis of eukaryotic microorganisms.
protocol, software ....
can I compare chromosome by chromosome or all of the chromosomes at once
Question unclear, please elaborate. Specify which data you have and what exactly you aim to achieve. Make sure your question is not too broad, be as specific as possible.
I want to do a genome comparative study of a fungus, but the species have a different number of chromosomes, so how can I do
I assume you have sequence data for these chromosomes? You could start by using an aligner like LASTZ that can try to align chromosome sized sequences (http://www.bx.psu.edu/~rsharris/lastz/README.lastz-1.04.00.html ).