Table 1 Features used in the machine-learning framework.
From: Harnessing machine learning to guide phylogenetic-tree search algorithms
# Feature | Feature name | Details | Represented action | Tree considered |
|---|---|---|---|---|
1 | Total branch lengths | The sum of branch lengths in the starting tree | Shared for pruning and regrafting | Initial tree (a in Fig. 1) |
2 | Longest branch | The length of the longest branch in the starting tree | ||
3–4 | Branch length | The length of the branch that was being pruned or regrafted | Both pruning and regrafting | |
5 | Topology distance from the pruned node | The number of branches in the path between the regrafting and the pruning branches, not including these branches | Regrafting only | |
6 | Branch length distance from the pruned node | The sum of branches in the path between the regrafting and the pruning branches, not including these branches | ||
7 | New branch length | The approximated length of the new branch formed due to pruning (see Supplementary Note 1 for feature extraction details) | ||
8–11 | Number of species | The number of leaves in the four subtrees | Both pruning and regrafting | Each of the four subtrees (b, c, c1, c2 in Fig. 1) |
12–15 | Total branch lengths | The sum of branch lengths in the four subtrees | ||
16–19 | Longest branch | The length of the longest branch in the four subtrees |
