msprime
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tskit-dev
Simulate genealogical trees and genomic sequence data using population genetic models
I've been looking at the `algorithm.c` and `algorithm.py` files in `msprime` and noticed some differences. The `algorithm.c` file seems to use diploid as a default setting, which affects how the...
I have been exploring the functionalities provided by `msprime` for modeling spatially structured populations and have noticed that there isn't a sweep model available for such populations. I am interested...
The `replicate_index` input in `sim_ancestry` function https://github.com/tskit-dev/msprime/blob/main/msprime/ancestry.py#L1100 is used repeatedly in various functions, but it is not documented in the docstring or the msprime documentation, and its usage is unclear....
This would help with the sgkit build: https://github.com/pystatgen/sgkit/pull/1111#issuecomment-1686316377
Milan and Marion have inquired (in a private communication) about implementing population-specific recombination rates in msprime. I now have a few more technical thoughts about it, and I'll stick them...
Proposal for adapting `algorithms.py` (see #1993) such that we can track the number of samples each segment is ancestral to without having to rely on AVL tree `S`.
The current SLiM scripts in `verification.py` throw up a few errors when run with SLiM 4.0 (default installed version is the latest version of SLiM). For example, the concept of...
We currently track all breakpoints during the simulation using an AVL tree. We should profile once #2121 is done and see if this is a significant amount of our time....
Currently the SLiM mutation model always *stacks* mutations, i.e., adds them on to existing ones. Sometimes we'd like to do something different, e.g.,: - have a "last" stacking policy (so,...
