Hi Marc Domènech ,

You can perform constrained tree search via -g option to force a monophyly. As for the "hard monophyly" you refer to, your constraint tree file should include all taxa belonging to the monophyletic group AND at least one extra taxon that not belong to the group. This is because the method infers unrooted tree. See Advanced tutorial of IQ-Tree for constrained tree search.

Hi Cheng-Min Shi ,

Thanks for your answer. But I think your solution would only make my group monophyletic with respect to the extra taxon I added, but the rest of the taxa would be able to fall within the monophyletic group, right?

However, you gave an idea. I think if you add a polytomy in the constraint it means those taxa can move freely, so I could build a constraint tree with a big polytomy including absolutely all terminals except the ones I want to form a clade, which would come as a smaller polytomy from the big polytomy as a single lineage.

Hi Marc Domènech ,

A quick check of the explanation for constrained tree search in IQ-Tree tutorial suggests that constraining with one extra taxon together with your target group with do what you want. See the example at http://www.iqtree.org/doc/Advanced-Tutorial#constrained-tree-search. My understanding is that the extra taxon should belong a clade that is most closely related to your contained group. It is not necessary to include all members of the clade in which the extra taxon is included. Since (your-monophyly-group, extra-taxon) has defined a bipartition, a situation where the rest of the taxa falling within the monophyletic group is not compatible with this bipartition. May you do some simple experiments to see what comes out.

Hi Cheng-Min Shi , thanks again for your answer. However, as I mentioned adding only one external taxa just made my group monophyletic with respect to that taxa, but other species fell within my group. I also tried doing a constraint in the way I posted in the first answer and fortunately it worked.