The Gantt chart can track dependencies, including multiple dependencies. The issue is whether you've discovered all of your task interdependencies or not and whether you add them to the dataset when you find them missing. If you haven't and you don't, you'll be screwed no matter what tools or techniques you use.

It's also possible, and sane people do this, to use ranges instead of fixed times for your durations. This helps to discover risk (particularly of exceeding a deadline).