Introduce the GTRX model and add some information on morphological phylogenetics in IQ-TREE#13
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bqminh merged 8 commits intoiqtree:masterfrom Jun 3, 2025
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HS6986
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HS6986
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Dear IQ-TREE Developers, I've added in this PR some information on partitioned morphological phylogenetics in IQ-TREE. |
bqminh
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Jun 3, 2025
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Dear IQ-TREE Developers,
This pull request adds some descriptions of morphological models in the documentation.
I explicitly introduce the GTRX model, which is the multistate model with unequal rates. This model has been implemented in IQ-TREE before, but, possibly because of its several properties that require caution, it has not been documented. I introduce this model with several warnings.
In addition, I introduce the concept of the MkA model (Pyron, 2017) since this information might be useful for some users. It is a concept that, for binary morphological characters where
0s represent ancestral conditions and1s represent derived conditions, mainly neomorphic (absent/present) morphological characters (sensu Sereno, 2007), allowing asymmetrical frequencies in models would make sense (e.g., Pyron, 2017; Sun et al., 2018 (https://ms609.github.io/hyoliths/bayesian.html)).I would appreciate it if you could consider these changes.
Thank you very much for your time and support.