necom Documentation

Cut a tree using Dynamic Tree Cut.

Input:

• A Newick file containing a single tree.
• Branch lengths are used to compute node heights.

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:

• The --min-size option is required and must be a positive integer.
• --deep-split enables more aggressive splitting (default: off).
• --max-tree-height sets the maximum joining height; if omitted, 99% of the tree height is used.
• --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.
• Leaves that fall below the minimum cluster size are labeled as unassigned (cluster 0) and are still emitted.

Examples:

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

2. Enable deep split necom cut dynamic tree.nwk --min-size 10 --deep-split

3. Limit maximum joining height necom cut dynamic tree.nwk --min-size 10 --max-tree-height 0.5