Add "related software" section

[benjeffery]

For software that interoperates with tskit formats, e.g.:

• relate
• argneedle
• arginfer
• slendr

Others?

No code snippet or "see more" needed.

[jeromekelleher]

Some others off the top of my head:

• Espalier uses tskit, but not obvious you can get tskit output from scanning docs
• geonomics uses tskit internally, has some support for tskit output.
• egrm

This becomes a tricky exercise tbh, deciding what's using tskit "enough" to be worth a mention here. Should we list every repo on GitHub that uses msprime as a dependency?

[benjeffery]

This becomes a tricky exercise tbh, deciding what's using tskit "enough" to be worth a mention here. Should we list every repo on GitHub that uses msprime as a dependency?

The threshold for me is that they either ingest or emit tree sequence files. Or is that still leaving us with a rather wide acceptance?

[bhaller]

SLiM, certainly. Probably slendr (https://www.slendr.net) should be too; it actually provides an R-based front end to parts of tskit, as I understand it (@bodkan).

[hyanwong]

The SCAR paper (https://www.biorxiv.org/content/10.1101/2022.02.08.479599v1) reads ARGweaver output into tskit to aid with analysis. Not sure that counts as "software" though? Shame there isn't native tskit output for ARGweaver.

[jeromekelleher]

The threshold for me is that they either ingest or emit tree sequence files.

Not obvious that this is possible for espalier or genomics from the docs.

I don't think we should get bogged down on this - let's make it up to the downstream developers. If they want us to mention their software on tskit.dev, then we will in the way that they want. If they don't or just don't respond to us, then we won't.

We can reach out to some of them after the website is launched.

[hyanwong]

Probably worth revisiting this, if it's easy to make such a section. I completely agree with Jerome that we "make it up to the downstream developers. If they want us to mention their software on tskit.dev, then we will in the way that they want".

I would start by putting slendr and tskit_arg_visualizer on there, as both are heavily tied to tskit projects.

[bhaller]

@bodkan ping!

[bodkan]

Hello, thank you for the ping! I'd be quite honoured if the tskit website mentioned slendr. After all, without tskit (and pyslim/SLiM + msprime), there would be no slendr at all. :)

Just to clarify, are you talking about adding stuff to the "Ecosystem projects" here or somewhere else?

Either way, I'd be very happy to put together a short title, blurb, a tiny example script, or whatever you envision for this to look like (I don't want to push this free advertisement opportunity too much, so just let me know).

[jeromekelleher]

We'd be delighted to promote slendr here @bodkan, please advertise as much as you like!

[hyanwong]

Just to clarify, are you talking about adding stuff to the "Ecosystem projects" here or somewhere else?

I think the idea was a new "related projects" section. @benjeffery ?

Either way, I'd be very happy to put together a short title, blurb, a tiny example script, or whatever you envision for this to look like (I don't want to push this free advertisement opportunity too much, so just let me know).

Great, thanks. We'll get back to you about the format. Nothing complicated!