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gphocs-dev / G-PhoCS

G-PhoCS is a software package for inferring ancestral population sizes, population divergence times, and migration rates from individual genome sequences.
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monomorphic sites #75

Open glaudelrio opened 3 years ago

glaudelrio commented 3 years ago

Hi! I was able to create a sequence file from my VCF. Is there a problem to run G-PhoCS without monomorphic sites? Thank you!

igronau commented 3 years ago

The monomorphic sites are used by the model to get a scale of time (using an assumed mutation rate). If you remove them, you'll likely have trouble scaling branch length of the locus-specific genealogies.

glaudelrio commented 3 years ago

awesome! I will go back and use my entire RAD loci with variant and monomorphic sites. Thank you!