necom Documentation

Construct a phylogenetic tree using UPGMA.

Input:

• A PHYLIP distance matrix (relaxed or strict).

Output:

• A rooted Newick tree.

Notes:

• UPGMA assumes an ultrametric (molecular clock): all leaves are equidistant from the root.
• When the input distances violate ultrametricity, the tree is still produced; negative branch lengths are clamped to 0 so the output remains a valid Newick tree.
• For non-ultrametric data, consider necom clust nj (neighbor-joining) instead.

Examples:

1. Build tree from matrix necom clust upgma matrix.phy -o tree.nwk

2. Pipe matrix from stdin cat matrix.phy | necom clust upgma stdin > tree.nwk