added comment to resolve polytomies that explains the missing resolution in some cases
@@ -371,7 +371,11 @@ class TreeTime(ClockTree):
"""
Resolve the polytomies on the tree.
The function scans the tree, resolves polytomies in case there are any,
- and re-optimizes the tree with new topology.
+ and re-optimizes the tree with new topology. Note that polytomies are only
+ resolved if that would result in higher likelihood. Sometimes, stretching
+ two or more branches that carry several mutations are less costly than
+ an additional branch with zero mutations (long branches are not stiff,
+ short branches are.)
Parameters
----------
