msprime
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tskit-dev
Simulate genealogical trees and genomic sequence data using population genetic models
The sectioning for the mutations page isn't working very well I think, and needs a bit of work. In particular, there's an awful lot of stuff under the "model" section,...
I'm using SLiM to simulate populations undergoing a lot of fission events, and I would like to use the function [`recapitate`](https://tskit.dev/pyslim/docs/latest/python_api.html#pyslim.recapitate) in pyslim to obtain fully coalesced tree sequences, but...
@petrelharp and I had an extended convo in Slack this week about silent mutations and the complications they introduce for users. I have some strong opinions about changes we could...
I've had some feedback from a new user that it'd be nice to have a "prerequisites" section that explains how much python you're going to need to know to use...
A simplification made in #1846 was to disallow samples that are internal nodes in the pedigree (i.e., samples cannot have children). It would not be difficult to implement, it just...
I think by default when running `sim_ancestry` we set `ts.tables.populations.metadata_schema` to something that requires a name and description. If I do a search in the docs for "schema", I can't...
(This is related to #2024) The docs for `recombination_rate` under `sim_ancestry` state: ``` See the [Recombination](https://tskit.dev/msprime/docs/stable/ancestry.html#sec-ancestry-recombination) section for usage examples for this parameter and how it interacts with other parameters....
I'm pretty sure `sim_mutations` is accumulating some garbage same as pyslim (see [#pyslim211](https://github.com/tskit-dev/pyslim/issues/211#issue-1070866233)). Note how `sim_mutations` also calls `ts.tables`. I don't have the bandwidth right now to make a proper...
We are interested in simulating the effect of differing recombination on some population genetics methods. It would be useful to extend the demographic model to include a 'change recombination rate'...
