necom Documentation

Calculate distances between nodes or generate distance matrices.

Input:

• A valid Newick tree file.
• If the file contains multiple trees, only the first tree is processed.

Notes:

• Modes (--mode / -m):
  • root (default): distance from each node to the root. Output: Node \t Distance.
  • parent: distance from each node to its parent. Output: Node \t Distance.
  • pairwise: distance between every pair of selected nodes, including self-pairs and both (i, j) and (j, i) orderings. Output: Node1 \t Node2 \t Distance.
  • lca: distance from each node in a pair to their Lowest Common Ancestor (LCA), for all selected-node pairs. Output: Node1 \t Node2 \t Dist1 \t Dist2.
  • phylip: a PHYLIP-formatted distance matrix for the selected nodes.
• Use -I to exclude internal nodes and -L to exclude leaf nodes.
• Use -n / -l / -x to restrict reported nodes to a name, name-list file, or regex.
• When no name-based filter is given, all selected nodes (respecting -I/-L) are reported.
• --mode phylip requires all selected nodes to be named; node names cannot contain whitespace characters.

Examples:

1. Distances to root (default) necom nwk distance tree.nwk

2. Pairwise distances necom nwk distance tree.nwk --mode pairwise

3. Generate a PHYLIP matrix necom nwk distance tree.nwk --mode phylip > matrix.phy

4. Distances to parent for leaves only necom nwk distance tree.nwk --mode parent -I

5. Distance to root for selected nodes necom nwk distance tree.nwk --mode root -n Homo -n Pan