How to understand `monomorphic sites`?

sanger-pathogens / snp-sites

Finds SNP sites from a multi-FASTA alignment file

http://sanger-pathogens.github.io/snp-sites/

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How to understand `monomorphic sites`? #107

Open xuechunxu opened 2 years ago

xuechunxu commented 2 years ago

Hi,

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

Best

CarolineOhrman commented 2 years ago

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.