Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.
get_distance(target, target2, topology_only=True) returns (according to the documentation) the number of nodes on the path between target and target2. Without the flag topology_only=True, it returns the branch length sum between the two targets.
It therefore seems more intuitive to return the number of edges connecting the two targets if topology_only=True.
It especially seems odd that two nodes connected by an edge have distance 0.
get_distance(target, target2, topology_only=True)returns (according to the documentation) the number of nodes on the path between target and target2. Without the flagtopology_only=True, it returns the branch length sum between the two targets. It therefore seems more intuitive to return the number of edges connecting the two targets iftopology_only=True. It especially seems odd that two nodes connected by an edge have distance 0.