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I've been trying to run a coalescent simulation using a standard model from the library - but instead of the default Hudson model, I want the simulation to use the discrete-time-Wright-Fisher model fo…
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Is there a method when simplifying a tree sequence to remove all unary nodes except the recombination nodes (a middle ground between ts.simplify(keep_unary=False) versus ts.simplify(keep_unary=True))?…
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Ideally we'll have a few stand-alone example scripts (eg as contributed by @hyanwong in #48 ) but these will:
1. not be too complex involving lots of library-ish code and new objects or functions t…
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Complete sweeps, sweeps from standing variation, and incomplete sweeps.
It'd be nice to do recurrent complete sweeps as well?
Need:
Analytical results
msprime for comparison (only currently possi…
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In #1573 we added the idea of a "duration" to ancestry models, which determines the maximum amount of time we can run. There was also some clarification in the docs about models that will run until fu…
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Right now pi is only generated at the tips using abundance and therefore assuming no incomplete lineage sorting. Since we have the tree we could construct a giant coalescent model and simulate data at…
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We have an extra unused parameter in the get_ll_representation for each DemographicEvent class. This is needed because stdpopsim will uses this until msprime 1.0 is released. Stdpopsim should then tra…
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Lots of nice new ideas are coming up on slack. Two initial entries for the FAQ could be
* #663
* coordinate system conventions for stdpopsim/msprime/SLiM/VCF/BED/GFF3
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Hi,
I'm having issues converting my Demes graphs to msprime `Demography` objects; both population sizes and migration rates are missing unexpectedly. My Demes graphs match what I think I'm trying t…
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Many species are partial selfers; for instance *C. elegans* (see #834) has a selfing rate of about 99.9%. SLiM has a "selfing rate" option that we can use directly; for msprime we'd need to rescale th…