If you wish the nodes to be stored in a database, then I'd suggest reading (and understanding) Nested Set Trees. In the common case of insert occasionally, query often, they are far more efficient than the usual adjacency model that people think of.
Unfortunately I don't know of a module that automates generating them in Perl, and I'm not entirely sure what such a module should look like. (Which may be why I don't know of one...) So you'd have to do some reinvention, but at least you'd reinvent a good version.
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