necom Documentation

Cut a tree using Dynamic Hybrid Cut.

Input:

• A Newick file containing a single tree.
• A distance matrix file in relaxed PHYLIP format (--matrix).

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 --matrix and --min-size options are required. --min-size must be a positive integer.
• --max-pam-dist sets the maximum distance for PAM reassignment (optional).
• --no-pam-dendro disables dendrogram respect during PAM reassignment (default: off).
• --deep-split enables more aggressive splitting (default: off).
• --max-tree-height sets the maximum joining height; if omitted, defaults to ref_height + 0.99 * (max_height - ref_height), where ref_height is the 5th percentile of merge heights and max_height is the maximum merge height.
• --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.

Examples:

1. Hybrid cut with min cluster size 20 necom cut hybrid tree.nwk --matrix dist.phy --min-size 20

2. Allow PAM reassignment across high branches necom cut hybrid tree.nwk --matrix dist.phy --min-size 10 --no-pam-dendro

3. Limit PAM reassignment distance necom cut hybrid tree.nwk --matrix dist.phy --min-size 10 --max-pam-dist 0.3