msprime
msprime copied to clipboard
tskit-dev
Simulate genealogical trees and genomic sequence data using population genetic models
I've already simulated 22 autosomes for ~1.5M samples using the [`FixedPedigree`](https://tskit.dev/msprime/docs/latest/api.html#msprime.FixedPedigree) model and I'm wondering about how much work might be required to simulate sex chromosomes. We are planning on...
TIL that `snakemake` now has features "tool wrappers" which allows popular command line tools to be used more simply with `snakemake` workflows: https://snakemake.readthedocs.io/en/stable/tutorial/additional_features.html#tool-wrappers I wonder if users would like an...
Using new `tskit-book-theme` The only question I have is whether this is acceptable: 
Hello all, I am interested in simulating large "landscapes" of connected demes parameterized by species distribution models for neutral demographic inference in non-model species. A tough line I'm trying to...
The genic selection model is not giving the correct output when the starting frequency is high. The code to reproduce the plot below is [here](https://github.com/molpopgen/msprime_discoal_comparison), and the README discusses the...
Hello! I've installed msprime using pip, but am met with the following error when I attempt to import it into JupyterLab. Traceback (most recent call last): File "", line 1,...
The installation docs currently tell users to install to the conda root, which is a Bad Idea. Update the docs to use an environment, and put in an explicit warning...
As discussed in #2083 Since there is a use-case for this now though, we could probably actually implement the functionality within msprime and do it automatically like we do for...
Per discussion here https://github.com/tskit-dev/msprime/pull/2080#discussion_r912322118 Since there's some subtlety around ascertainment or not, we should document this point.
We need some reproducible statistical validation of the microsat mutation models in verification.py. Do we have analytical results we can compare to or to other simulators? Any thoughts @petrelharp @andrewkern?