add GTRspmix models

[HRD-Ryo]

Hi Minh,

I have added the explanations for GTRspmix models.
Currently, the citation is commented out because we are working on the manuscript and preparing to submit the ms to bioRxiv. I will update the citation with the preprint info as soon as it is posted. Could you please review the text and structure first?

Ryo

[bqminh]

Looks good. But I will have to wait until a version of IQ-TREE is released with these models. Right now it's in the GitHub code, but not released yet in the iqtree website

[bqminh]

This will be merged once there is a new release of IQ-TREE with these models

[bqminh]

Can you also add a section about how to use GTRspmix in this document: https://iqtree.github.io/doc/Estimating-amino-acid-substitution-models. After the section about GTRpmix.

[HRD-Ryo]

I don't think GTRspmix requires any special instructions in the IQ-TREE manual, as there are no dedicated flags for it.
Currently, the only way to optimize the model is through my Python wrapper script, which I will be releasing as a separate GitHub repository later.

Or should we add broad introduction and simplest command example?
like:
iqtree3 -s <alignment> -m S28pfamC60+G4

[bqminh]

Does your wrapper script offer a single command line to do the estimation? If yes, we can document it in that web page there. But it's up to you. I was just thinking how to best inform users, and thought that this page is a good pointer to the feature.

[HRD-Ryo]

That makes sense, and I agree it would be a great way to inform users.

By the way, I have just published the repository for the wrapper script at: https://github.com/HRD-Ryo/GTRspmix

To be honest, the estimation process is currently a bit complex. So, instead of putting long instructions on the IQ-TREE page, how about we just add a brief introduction (maybe few sentences) about the wrapper script and provide a link to the GitHub repository? Users can read the README there.

In the future, if IQ-TREE implements the native estimation functionality for GTRspmix model, I would be more than happy to write a manual for it.

If you agree, I can draft a short paragraph for the webpage.

[bqminh]

yes, that sounds good. Can you also change the citation to Banos et al in that web page along the way? It's outdated.

[HRD-Ryo]

I have edited the doc. Could you review it?