I am working with ETE3 and I stumbled upon an error that I have never retrieved before:
ete3.coretype.tree.TreeError: 'Nodes are not connected!'
The error seems to trace back to the
get_common_ancestor() function, which is in the
tree.py script of ETE3.
The lines raising the error are these, within a
IDs_to_keep = [ ID for ID in Relevant_ID_list ] ... Leaves_to_keep = [ t.search_nodes(name=leaf) for leaf in IDs_to_keep ] t.prune(Leaves_to_keep)
I should probably also mention that not every phylogenetic tree arises this behavior. It is running smoothly for most of the phylogenetic trees in the list I have, and only rarely encountering this error! The internet is quite scarse on the subject and I don't really know what's going on. Can anyone help me?