necom Documentation

Rename nodes in a Newick tree.

Input:

• A Newick tree file.

Notes:

• For nodes with names, use --node.
• For unnamed internal nodes, use --lca with two comma-separated names.
• The total number of --node and --lca arguments must equal the number of --rename (-r) arguments.
• Matching order: the first N --rename values are applied to the N --node arguments in order, and the remaining --rename values are applied to the --lca arguments in order. The order in which --node, --lca, and --rename arguments appear on the command line does not affect this matching.
• This command is designed for small edits, not batch replacement. For batch replacement, use necom nwk replace or external tools such as sed or perl.

Examples:

1. Rename a named node necom nwk rename tree.nwk --node Homo --rename Human

2. Rename an internal node via LCA necom nwk rename tree.nwk --lca Homo,Pan --rename CladeX

3. Rename multiple nodes necom nwk rename tree.nwk \ --node Homo --rename Human \ --lca Homo,Pan --rename CladeX