necom Documentation

Extract labels (names) from a Newick file.

Input:

• A Newick tree file.

Notes:

• By default, prints all non-empty labels in Newick order, one per line.
• Use --root to print only the root label.
• Use --tab / -t to print labels on a single line separated by tabs.
• Use -I to exclude internal nodes and -L to exclude leaf nodes.
• Selection options (-n, -l, -x) can be combined.
• With -D, descendants of selected internal nodes are also included.
• -M verifies that the selected nodes form a clade with at least two nodes.
• Duplicate node names may affect selection and clade checks.
• Extra columns (-c / --column):
  • dup: duplicate the node name.
  • taxid: :T= field from the comment.
  • species: :S= field from the comment.
  • full: full comment.

Examples:

1. List all labels necom nwk label tree.nwk

2. Count leaves necom nwk label tree.nwk -I | wc -l

3. List specific nodes necom nwk label tree.nwk -n Human -n Chimp

4. List labels matching a regex necom nwk label tree.nwk -x "^Homo"

5. Check clade necom nwk label tree.nwk -n Human -n Chimp -M