[Feature Request] Allow multiple tree constraints

[HS6986]

Dear IQ-TREE Developers,

I'm running IQ-TREE v2.3.6 with topological constraints and I've realized that IQ-TREE doesn't allow multiple tree constraints; it recognizes only the first tree that appears in a constraint file. It may sound strange to set constraints by multiple trees, but this is because I want to set floating taxa (taxa not included in a constraint) separately for each constraint. This is not a problem in MrBayes, TNT, or TreeSearch, the other phylogenetic analysis software I have primarily used, because they provide features to set floating taxa separately for each constraint.

Here's the folder of my IQ-TREE reanalysis of a morphological dataset from Shao et al. (2020) with constraints, showing that IQ-TREE doesn't consider multiple tree constraints.

This feature is needed for my research. I would greatly appreciate it if you could implement it in a future IQ-TREE release, if possible.

P.S. Since I want to analyze morphological datasets in a maximum likelihood framework to compare the results between phylogenetic analysis methods, I also checked RAxML-NG and it shows the same behavior as IQ-TREE (reported in amkozlov/raxml-ng#206).

[bqminh]

This is not easy, rather quite difficult, to implement as it may sound. Especially, if different constraint trees contain different sets of taxa. Currently I don't know which algorithm to use, even at the initial step of constructing an initial tree that obeys all constraints....

[HS6986]

Thank you for considering how to implement this feature. I understand it is probably a difficult one to implement. I'm sorry, but I don't have any knowledge about the implementation of it in other software.