necom Documentation

Perform agglomerative hierarchical clustering on a distance matrix.

Input:

• A PHYLIP format distance matrix (strict or relaxed).
• For pairwise list input (name1\tname2\tdist), use necom mat to-phylip first.

Output:

• A Newick tree string written to stdout or --outfile.

Notes:

• Internal node height is half the linkage distance (height = distance / 2); branch length from child to parent is parent_height - child_height.
• --method <METHOD>: linkage method (default: ward). Supported: single, complete, average (upgma), weighted (wpgma), centroid (upgmc), median (wpgmc), ward (ward.d2).
• For reducible methods (single, complete, average, weighted, ward), the default NN-chain implementation may produce a different merge order than the primitive algorithm, but the resulting partition sequence is equivalent.
• centroid and median linkage may produce non-monotonic merge heights (inversions); branch lengths are clamped at 0.0 so the resulting Newick tree remains valid. The same clamp is applied to all methods as a safety net.
• For Ward’s method, the input is assumed to be Euclidean distances or similar.
• Alias: necom clust hclust is equivalent to necom clust hier.

Examples:

1. Ward’s method (default) necom clust hier matrix.phy > tree.nwk

2. Average linkage (UPGMA) necom clust hier matrix.phy --method average > tree.nwk

3. Single linkage (nearest neighbor) necom clust hier matrix.phy --method single > tree.nwk