Prevent IQ-TREE from automatically removing missing states from the Markov process

[HS6986]

Dear IQ-TREE Developers,

This problem is almost identical to iqtree/iqtree2#454.

I'm conducting a partitioned phylogenetic analysis of the morphological dataset of Luo et al. (2025) using IQ-TREE v3.0.1. However, unfortunately, in the 8-state partition, some states were removed from the Markov process with a message NOTE: State(s) 1, 3, 4, 6 not present in partition part8 and thus removed from Markov process to prevent numerical problems. This underestimated the size of state space in the partition. Creating a partition file with the data type for each partition specified as MORPH{n} and specifying it did not help.

The commands used were as follows:

iqtree3 -p Matrix -st MORPH -m MFP+ASC -T 6 --prefix NoPartitionFile
iqtree3 -p Partitions.nex -st MORPH -m MFP+ASC -T 6 --prefix WithPartitionFile --redo

My question is: is there a way to explicitly prevent IQ-TREE from removing missing states from the Markov process? If not, implementing such a feature would be highly useful. I think that at least if the MK model was specified as the model for every partition, there would be no numerical problems due to missing states.

Here's the folder of the analysis.

Thank you very much for your time and support.

[HS6986]

Sorry, from information in other analyses, I've noticed that the missing states are only removed from the Markov process and are properly reflected in the model. Sorry for the confusion I may have caused. I am closing this issue now.