Unrooted Tree Splitting Species


I am working with around 50 Staphylococcus isolates of 6 different species. When I create my tree one species is getting split into two branches. The species differs depending on whether I’m running fast or accurate. I also tried removing some of the references, which resulted in different species splitting into two branches (see quick visualization below, two have the same number of references and were just ran with fast vs accurate, one was run on fast and has more references).

Are there any recommendations on how to get a visualization where they all group, as they do when you consider the trees as a whole? Do I need to root it?