msprime

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Experimental yaml input format

7

This is an experiment to see what a yaml/json input format (building on demes) would look like. It mostly works I think, except for the basic confusion about the direction...

jeromekelleher

We should be able to implement models of (independent) codon sequence evolution following the approaches of [Arenas and Posada 2007](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-458) It's not entirely satisfactory that we'll end up with independent...

jeromekelleher

Comments on page /demography.html

3

Not an 'issue', just a log of some comments I'm making while reading this page. > In continuous-time models, when {math}`M_{j,k}` is close to zero, this rate is approximately equivalent...

gtsambos

Decouple trajectory from sweeps

1

I'm finding the time and population size conversions in the sweeps model super confusing, and I would *really* like to decouple the trajectory simulation from the sweep definition. I don't...

jeromekelleher

Initial outline for Trajectory refactoring

4

Here's a rough outline for what I'm thinking the low-level C will look like. I think it's worth getting things right here in the Python version before looking at the...

jeromekelleher

Class design for "selective sweep" concept.

10

This issue is motivated by #1762 The current class for modeling the [structured coalescent](https://pubmed.ncbi.nlm.nih.gov/3066685/) is `msprime.SweepGenicSelection`. This class handles the following scenario: * Given a start/end frequency (e.g., moving backwards...

molpopgen

coalescent_rate_trajectory and friends assumes diploidy

1

As pointed out in #1761, these functions assume diploidy. Fixing this would just require adding a `ploidy` argument that replaces the `2` right [here](https://github.com/tskit-dev/msprime/blob/d247ed2c43cbe22d10a66e862b6693db184b1203/msprime/demography.py#L4272).

petrelharp

verification script does not cover the case of sweeps from standing variation.

1

Related to #1762, `verification.py` only considers sweep models with initial frequencies of 1/2N.

molpopgen

"Sandbox violation" with meson 0.57

3

Looks like our C library build is broken by meson 0.57. The recommended approach for now is to make sure you have an older version installed: ``` python3 -m pip...

jeromekelleher

Clarity docs for population_size and initial_size

2

It [looks to me](https://github.com/tskit-dev/msprime/issues/1734#issuecomment-861600728) as if the population_size and initial_size parameters are specified in number of individuals, not number of genomes. That is, they depend on the "ploidy" setting. For...

hyanwong