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dekoning-lab / slim-tree

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Should we increase the default length of the burn-in? #75

Open ebrintn opened 1 year ago

ebrintn commented 1 year ago

I am noticing there is a lot more dN than dS, even when mutation is weak. I think we need to increase the burn in from 1000 to at minimum 10 thousand generation. This should be ok because the software is faster now!

ebrintn commented 7 months ago

@jasondk I think this may be worthwhile - I've managed to speed up a lot of things and am noticing that populations tend to be deversifying until about generation 10000

ebrintn commented 3 months ago

I'm not sure if we need to expand the burn in because the dn/ds values of neutral evolution are not 1 for p1. @jasondk what are your thoughts?