How to understand `monomorphic sites`?

[xuechunxu]

Hi,

Could you please show some examples to help us understand the parameter -b?
-b output monomorphic sites, used for BEAST

Best

[CarolineOhrman]

My impression is that the default is to output monomorphic sites but when the -b option is used these are skipped. The parameter description should be changed if this is the case.