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add GTRspmix models#22

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add GTRspmix models#22
HRD-Ryo wants to merge 1 commit into
iqtree:masterfrom
HRD-Ryo:HRD-Ryo/GTRspmix

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@HRD-Ryo
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@HRD-Ryo HRD-Ryo commented May 19, 2026

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

citation will be added
@HRD-Ryo HRD-Ryo marked this pull request as ready for review May 19, 2026 08:13
@bqminh
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bqminh commented May 21, 2026

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

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bqminh commented May 23, 2026

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

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bqminh commented May 25, 2026

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.

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HRD-Ryo commented May 25, 2026

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

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bqminh commented May 25, 2026

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.

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