skbio.root_at_midpoint hits recursion limit on large trees

[gregcaporaso]

This method hits the recursion limit on very large trees (I hit it on a tree with around 3m tips). We should fix this, or at least provide a more useful error message (current error is not useful to users: RecursionError: maximum recursion depth exceeded).

In the meantime, I work around this limitation by doing midpoint rooting with ete3 as follows:

from ete3 import Tree
t = Tree("combined-ssu-align/combined-ssu-align.bacteria.mask.tre", format=1)
t.set_outgroup(t.get_midpoint_outgroup())
t.write(outfile="combined-ssu-align/combined-ssu-align.bacteria.mask.mid-rooted.tre", format=1)

This issue was first noticed in connection with #1077.

[JTFouquier]

Thanks @gregcaporaso for this! I was pretty lost. A better warning here would have be very helpful.