Synteny diversity calculation

[Li-Chengyu]

Hello wen-biao,
I'm trying to compare the degree of genomic rearrangements among a reference genome P and several related query genomes C1-C3. I don't fully understand the files used in step1 (pairwise whole genome alignment and synteny identification) you've described. Are these files included in the folder pairwiseWGA the delta files generated by MUMmer4? or some other files?
Also, I just want to make comparisons between the genoem P and each query genome C, escaping the pairwise comparisons within query genomes, so is it OK to use your scripts? Or, do I need to modify some command lines in the scripts?
Looking forward for your reply!

Best wishes,
Chengyu