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tskit-dev / tutorials

A set of tutorials for msprime and tskit.
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Interoperating with Dendropy tutorial #141

Open jeromekelleher opened 2 years ago

jeromekelleher commented 2 years ago

With some updates coming down the pipeline in tskit (https://github.com/tskit-dev/tskit/projects/9) we should soon be able to resolve the long-standing issue of interoperating with existing phylogenetics methods. It would be really nice if we could give a short tutorial showing how to run (say) a simulation in msprime, and then export the trees and alignments to Dendropy, doing some simple operations.

@jeetsukumaran I'm not sure of you've seen the "tskit tutorials" site, here: https://tskit.dev/tutorials/intro.html

The idea is the build a set of tutorials on using tskit using JupyterBook. It's a work in progress, but there's already a lot of great content in there, I think.

Since this workflow is what you're mainly interested in doing, I think it'd be great to capture your experience here in a short tutorial. What do you think?

jeetsukumaran commented 2 years ago

This is a really nice idea. I would be happy to contribute. Most likely after we sort out the nexus output, of course. I'm a bit old school and don't use Jupyter (Vim + shell for me :) ), but I can try to adapt to the 2020's ...

jeromekelleher commented 2 years ago

I'm a bit old school and don't use Jupyter (Vim + shell for me :) ), but I can try to adapt to the 2020's

Likewise! vim+tmux is the ultimate IDE as far as I'm concerned :smile: