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?
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?