Qualify let’s you define multiple concurrent application definitions each with their own data stores, terminology, permissions and workflows. You can choose from any of the supplied templates and modify them if desired or create your own model that exactly matches your own work processes.
If you need disparate methodologies but still need a consolidated view of say Requirements or Issues, these can be defined at a global level and used by all the methodologies.
So agile, waterfall or your own hybrid methodology. You can have them all, and at the same time.