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Reading large trees in DendroPy results in a huge call stack. Increase the recursion limit now to prime ourselves for fully dated trees,
We don't write to output files in parallel, so we don't need to hold them open all at once. Break up with block to only open the relevant file when writing.
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Some small bits that were floating around in my work tree that could be merged.
The latter despite it's size doesn't change any logic, just break up the big
with open(...), see the diff ignoring whitespace