I have a number of synteny blocks from two genomes comparison and I would like to conduct some kind of a statistical test on how each block is significant as opposed to being there by chance.
Now, if this was the only case, I can perform a permutation test on how likely to get x number of genes from one genome as a group of homologs with respect to the other genome, right? However, the synteny from each genome could contain some few genes that are not homologous, and I am not sure how to incorporate these into the test? I don't think that the test is valid if I will ignore these non homologous genes and consider only homologous genes.
I hope my question is clear (if not please let me know) and I am looking forward to any suggestions or ideas in approaching this.
Thanks in advance.