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                                            Megan Smith

Inferred tree does not have the highest quartet score

Hi Siavash, Thanks for the quick reply. The score for the FASTRAL tree is 12425305589, so it is receiving a better quartet score than the ASTRAL (12380755710) tree as well,...

Monomorphic sites with VCF from stacks

Hi Isaac, Thanks for the quick response! That is what I was asking. Hmm, I think the monomorphic bin should include complete sequence length (corrected for downsampling) minus the number...

Monomorphic sites with VCF from stacks

Hi Isaac, I think you’re correct that the best way to do this is to add a command line flag to pass in total sequence length. Not sure what changes...