necom Documentation

Cut a tree using a static threshold method.

Input:

• A Newick file containing a single tree.
• Branch lengths are used by distance/height-based methods.

Output:

• --format cluster (default): each line contains the members of one cluster; the first member is the representative.
• --format pair: each line contains a (representative, member) pair.

Notes:

• Exactly one method option must be provided: --k, --height, --root-dist, --max-clade, --avg-clade, --med-clade, --sum-branch, --leaf-dist-max, --leaf-dist-min, --leaf-dist-avg, --max-edge (--single-linkage), --inconsistent.
• --k must be a positive integer.
• --deep controls the depth used by the inconsistent method (default: 2).
• --rep selects the cluster representative: root (default), first, or medoid.
• --support <S> treats edges with support < S as effectively infinite length, forcing a cut at low-support positions. Nodes without explicit support default to 100.0.
• Distance/height thresholds must be non-negative finite numbers.

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. Cut by max pairwise distance necom cut simple tree.nwk --max-clade 0.1

4. Use pair format necom cut simple tree.nwk --k 3 --format pair