necom Documentation

Extract a subtree (clade) rooted at the lowest common ancestor (LCA) of the selected nodes.

Input:

• A Newick tree file.

Notes:

• Node selection: use -n for exact names, -l for a name-list file, or -x for a regular expression. If no selection is provided, no output is generated.
• -M: ensure the selected nodes form a clade with at least two terminal nodes.
• --condense / -C: instead of extracting the subtree, replace it with a single node in the original tree. The new node inherits the edge length of the subtree root and receives annotations member=<count> and tri=white.
• --context / -c: extend the subtree by N levels above the LCA.

Examples:

1. Extract a subtree for two nodes necom nwk subtree tree.nwk -n Human -n Chimp

2. Extract a subtree for nodes matching a regex necom nwk subtree tree.nwk -x "^Homo"

3. Condense a clade into a single node necom nwk subtree tree.nwk -n Homo -n Pan --condense Hominini

4. Check if a group is a clade necom nwk subtree tree.nwk -n Human -n Chimp -n Gorilla -M