I think the phrase (instead of 'obfuscated') you want is 'general, debugged, maintained, comprehensive and written by someone else so I don't need to bother'.

Probably Bio::Phylo::IO (the module you would actually use) doesn't use exactly the structure you currently use (or think you would like to use) for the internal representation of the trees. But it is likely that the structure the module uses is more generally useful and that the work you want to perform on the structure is already supported among the Bioperl modules.

Update: It is true I've not used Bioperl modules. I looked at the docs for a few before I answered and on the face of it they seemed at reasonably documented. I was reacting to what appeared to me to be a "modules are too complicated" and NIH attitude in the OP's node. My apologies.

I think the phrase (instead of 'obfuscated') you want is 'general, debugged, maintained, comprehensive

Here's an alternative phrase based on my experience of trying to use Bioperl modules:

Nearly impossible to install; complicated, over-engineered, incomprehensible, slow and buggy.

---

Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.

"Science is about questioning the status quo. Questioning authority".

In the absence of evidence, opinion is indistinguishable from prejudice.

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This comment makes it clear that you have never used Bioperl. Doing so is almost always a mistake.

Update: Let this be a lesson to those of you eager to mindlessly parrot the Perlmonks orthodoxy. Don't do so unless you have experience in the relevant domain.