Building on top of this existing library and package infrastructure has huge advantages. For example, here's some code where we load the Wide ARG, and simulate 1.4 million mutations under the Felsenstein 84 model using #msprime (params arbitrary). This takes 2.5 seconds.

Ultra-realistic simulations of 1.4 million human genomes generated by using a detailed pedigree of French Canadians as input to #msprime! These simulations are hugely useful for large-scale genomics methods development, because they are freely available, easy to download (2.8G for chr1), and efficient to process using #tskit. I hope they will become a standard benchmark across all sorts of methods.

https://www.science.org/doi/10.1126/science.add5300

Here's the repo on GitHub for the ARG visualizer which plots a #tskit tree sequence using D3.js:

https://github.com/kitchensjn/tskit_arg_visualizer

You will need #jupyter, #msprime, and #numpy installed in Python to run the notebook. Let me know if you have any issues getting it running.

There are so many rules around node positions and paths between nodes. I'm slowly picking through a document of scenarios that break the current implementation. More updates to come!

I've collected all of my #msprime/#tskit/demes visualizations into one place: https://observablehq.com/collection/@molpopgen/coalescent-theory

A work in progress visualizing trees under simple models of population splits and migration: https://observablehq.com/@molpopgen/simple-model-of-a-population-split-with-symmetric-migratio

Here, #msprime and #tskit do a lot of the work, but demes (https://popsim-consortium.github.io/demes-spec-docs/main/tutorial.html) handles the hard work of defining the demographic models.

Barely keeping ahead of my class. Here's a visualization of how variable tree sequences can be due to recombination. This is #msprime and #tskit in a browser.

https://observablehq.com/@molpopgen/coalescent-trees-with-recombination

@castedo @kitchensjn it had been a while, so I fired up one of the interactive #python visualizations from my site. It takes ages for the Binder stuff to spin up. I will recreate one of them with #pyodide and #msprime this week.

Here's an example of running #msprime in a browser and manipulating #tskit types in #JavaScript. The #Python code is all compiled to #wasm and run via pyodide.

https://observablehq.com/@molpopgen/coalescent-trees-without-recombination

Ready to demo this in class on Monday!

cc @kitchensjn