You can mark the out-group and reorganised the branches in the visualization step. It is post processing part during visualization and not the part of tree construction.

I think the problem is un choosing the outgroup , so be careful with the out group and try many out groups to fit your requirement .best wishes

For those genes, I would assume you are running NJ on mega, right? The NJ method produces an unrooted tree because it does not require the assumption of a constant rate of evolution. Are you setting manually what are the outgroups? Otherwise, the tree will be rooted in the mid-point. But you can also manually root the tree in your outgroup a posteriori, for visualization porpouses.

Thank you all 🌹🌹