necom Documentation

Cut a Newick tree into flat clustering partitions.

necom cut is split into five focused subcommands. Run necom cut <subcommand> --help for detailed options.

Input:

• A Newick file containing a single tree.
• Branch lengths are used by distance/height-based methods.
• Branch support values (optional) can be used as a non-crossable constraint via --support.

Subcommands:

• simple: static threshold methods such as k, height, max-clade, avg-clade, inconsistent, etc.
• dynamic: Dynamic Tree Cut (top-down adaptive, --min-size).
• hybrid: Dynamic Hybrid Cut (tree + distance matrix, --min-size, --matrix).
• scan-simple: parameter sweep over a static method threshold.
• scan-dynamic: parameter sweep over dynamic-tree min cluster sizes.

Examples:

1. Cut into 5 clusters necom cut simple tree.nwk --k 5

2. Cut at height 0.5 necom cut simple tree.nwk --height 0.5

3. Dynamic Tree Cut with min cluster size 20 necom cut dynamic tree.nwk --min-size 20

4. Scan thresholds and save statistics necom cut scan-simple tree.nwk --max-clade --range 0,0.5,0.01