necom Documentation

Reroot a phylogenetic tree on a specific branch or node.

Input:

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

Notes:

• Target selection:
  • Default (no nodes specified): reroot at the midpoint of the longest branch.
  • --node / -n: reroot on the edge leading to the LCA of the specified nodes. The specified nodes become the ingroup.
  • --lax / -l: if the LCA of specified nodes is already the root, use the unspecified nodes as the ingroup instead. Useful for defining an outgroup by exclusion.
• Operations:
  • Reroot (default): creates a bifurcating root at the target edge.
  • --deroot / -d: converts a bifurcating root into a multifurcating root by collapsing its internal children into the root. Takes priority over --node and --lax (which are ignored when --deroot is given).
• --support-as-labels / -s: treat internal node labels as support values and shift them along the rerooting path to maintain split associations.
• Topology cleanup: the original root’s parent edge is merged, and degree-2 nodes created during the process are removed.

Examples:

1. Reroot at the longest branch (default) necom nwk reroot input.nwk

2. Reroot at a specific node necom nwk reroot input.nwk -n Homo

3. Reroot at the LCA of multiple nodes necom nwk reroot input.nwk -n Homo -n Pan

4. Reroot and preserve support values necom nwk reroot input.nwk -n Homo --support-as-labels