-b parameter explanation

[aminakur]

Could you please elaborate on the -b parameter usage? -b block_sizes comma-separated list of synteny block scales [default = 5000] What is a synteny block scale and how to find an optimal one for a particular analysis?

[mikolmogorov]

I suggest reading the Genome Research paper which have the algorithm description. There is no definite algorithm for choosing synteny block scale, but the default setting should work fine in most cases. If the particular parts of the paper are unclear - will be happy to help!