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Interoperating with Dendropy tutorial #141
Description
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?
Activity
jeetsukumaran commentedon Oct 19, 2021
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 commentedon Oct 20, 2021
Likewise! vim+tmux is the ultimate IDE as far as I'm concerned 😄
hyanwong commentedon Apr 28, 2026
@jeetsukumaran - I have just stumbled across this open issue, and am not sure what @jeromekelleher meant by interoperating? I assume that the default way to get trees into Dendropy from tskit is via Nexus, e.g. as in https://github.com/tskit-dev/tskit/blob/f268aefdc62e212765ff8d22ab1caa84fa24ec17/python/tests/test_phylo_formats.py#L1560. If so, I'm happy to add some of this to the phylogenetics tutorial.