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get_distance() with topology_only=True should return number of edges, not nodes (ete3) #741

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lenacoll opened this issue Feb 7, 2024 · 0 comments

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@lenacoll
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lenacoll commented Feb 7, 2024

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.

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