necom Documentation

Condense monophyletic subtrees whose leaves share the same taxonomic term at a selected rank into a single node.

Input:

• <infile>: Newick tree whose leaf labels match the first column of the taxonomy TSV. Use stdin for standard input.
• --taxon <taxon.tsv>: Tab-separated file without header, containing at least 2 columns:
  • Column 1: node name (must match leaf labels in the Newick file).
  • Column 2+: taxonomic terms (e.g., species, genus, family).

Output:

• Condensed Newick tree written to -o/--outfile or stdout.
• With --map, also writes condensed.tsv to the current working directory. It contains two tab-separated columns: original node name and condensed label.

Notes:

• Use --rank to select which column(s) of the taxonomy TSV to use for grouping (1-based index, default: 2).
• Multiple --rank values may be supplied to condense at multiple levels.
• Only monophyletic subtrees with the same taxonomic term are condensed; non-monophyletic groups are skipped.
• Condensed nodes are named {term}||{count}, where {count} is the number of leaves in the condensed group.
• Condensed nodes carry member=<count> and tri=white comments for visualization.

Examples:

1. Condense by species (2nd column) necom pl condense --taxon taxon.tsv tree.nwk

2. Condense by genus (3rd column) necom pl condense --taxon taxon.tsv --rank 3 tree.nwk

3. Condense by multiple ranks necom pl condense --taxon taxon.tsv --rank 2 --rank 3 tree.nwk

4. Output a mapping file alongside the condensed tree necom pl condense --taxon taxon.tsv --map tree.nwk -o condensed.nwk