msprime
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tskit-dev
Simulate genealogical trees and genomic sequence data using population genetic models
Summarizing an email chain as an issue to allow for open discussion of the topic. Mutations in telomeres and centromeres can lead to misleading results. So it makes sense to...
Now we have reference sequences (sometimes), and so `sim_mutations` should use this, when it is present. Recall that a mutation generator has two pieces: first, a way to [choose the...
A significant usability limitation in the 1.0 API is that we can't easily include mutations in a simulation with replicates. I think we could improve this by allowing sim_mutations accept...
#1599 introduced the idea of an "unknown" rate within a RateMap using NaNs. This solves a lot of problems, but it doesn't tell us how we should run the actual...
It would be handy to have a top-level function that does simple simulations of ancestry and mutations. How about we do something like ```python def sim( samples, *, sequence_length=None, recombination_rate=None,...
#1371 added some type annotations for data classes. We should also annotate the top-level functions, as much as we can (some will be a little convoluted). Also add some documentation...
sim_ancestry supports providing an arbitrary rate map as input, but the underlying infrastructure currently assumes a single rate and will trip some assertions. Waiting on #1196 first.
With the new provenance code there are some additional requirements for adding new methods or modifying existing ones, as I'm discovering over in #946. In figuring this out it'd be...
Run a performance analysis on the DTWF for a large simulation and see where the time is being spent. Since it seems like we're not using the Fenwick tree at...