IntelliGantt supports Bamboo Solutions nifty Task Master web part which lets you see parent/child relationships, task dependencies and milestones within SharePoint via your web browser. However, by default IntelliGantt uses the 'Tasks and Milestones' filter, which filters out summary tasks.
Because this creates a subset of all your tasks, IntelliGantt essentially 'flattens' the hiearchy-- because summary tasks are not shown there is no parent to set.
Similarly, if a filter is active, task dependencies are not shown because its either not clear or possibly even misleading to attempt a partial set of task dependencies.
Therefore, if you want to make use of all the Task Master features with IntelliGantt (both the desktop and the MS Project Add In) you will want to make sure the filter in the Workspace Settings is set to 'Show All Tasks'. By default it is 'Tasks and Milestones'.
Here's a screenshot of what you want to set:
To access this in IntelliGantt, select a project, right-click and choose 'Workspace Settings'.
To access this in the IntelliGantt Add In for MS Project, drop down the 'IntelliGantt' menu to the 'Project' menu flyout and choose 'Settings'.
Also, be sure to activate the 'Milestone' field so that milestone information is sent to the Task Master. This maps to any zero duration task in IntelliGantt. In the Add In, its any zero duration task or any task marked 'true' for the MS Project Milestone field.
Finally, if you consistently work with the Task Master, you may want to click the 'Save as Default' checkbox at the bottom of the Workspace Settings. This will save your current settings and apply them to all new IntelliGantt projects going forward-- like Task Filter.