Haag et al. measure the ruggedness of a tree landscape by training a regression model (trained on molecular datasets, implemented in C) based on:
- Unique topologies after 100 parsimony searches: 42.9 %
- RF-Distance between parsimony trees: 33.2 %
- Entropy (Average Shannon entropy per column): 17.0 %
- Patterns (unique columns)-over-taxa 13.6 %
- % Gaps 2.5 %
- Bollback 2.3 %
- Sites(n columns)-over-taxa 1.5 %
- % Invariant columns 0.6 %
Haag et al. measure the ruggedness of a tree landscape by training a regression model (trained on molecular datasets, implemented in C) based on: