Like Indexing Tuning Wizard, you can also use DTA to analyze your queries. However, the way to invoke that is not obvious, because you cannot do it directly from within DTA.
You need to have the query open in the Query Window of Sql Server Management Studio first. Go to the Query menu, then pick Analyze Query in Database Engine Tuning Advisor. This will open DTA. After connection, you will see Query radio button is selected in the Workload area. The Query Radio button is not visible if you open DTA directly from Start -> Programs.