In this sort of work one is quickly realizes that no software package does everything. One has to pick the software to get the job done. Since it's research software, one has to develop a high pain threshold.
I chose Language Explorer (a.k.a. Fieldworks, Flex, ...) for morphosyntactic analysis and Elan for time-alignment. I could nitpick about either of these programs for hours, but the fact is that they provide the utilities that I need, and I'm not aware of anything better. Replicating their functionality in a manner better suited to my needs would take months of work.
The pertinent restrictions:
One would typically imagine that getting two pieces of software written independently of one another to talk to another would be a task best consigned to the inhabitants of the ninth circle of hell. But there is grace, since both of these programs store data in XML format. Therefore it is more an eighth-circle-of-hell task.
When I wrote my fellowship application I noted that I am familiar with XSL. At the time it seemed even to me something of an idle boast; little did I know that it would end up being crucial to the project.
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