necom Documentation

Compare trees using Robinson-Foulds (RF) distance and its variants.

Input:

• One file: compares all trees in the file against each other (pairwise).
• Two files: compares each tree in the first file against each tree in the second file.
• Use "stdin" to read from standard input (only one of the two files may be stdin).

Output:

• TSV with columns Tree1, Tree2, RF_Dist, WRF_Dist, KF_Dist.
• Tree IDs are 1-based indices of the trees in the input files.

Notes:

• Metrics:
  • RF: Robinson-Foulds distance (topological difference).
  • WRF: Weighted Robinson-Foulds distance (branch length difference). Trivial splits (single-leaf branches) are excluded by default.
  • KF: Kuhner-Felsenstein (Branch Score) distance. Trivial splits are excluded by default.
• Use --include-trivial to include single-leaf splits in WRF/KF calculations.
• Single-file pairwise mode requires at least 2 trees; with fewer, the command errors out with a clear message.

Examples:

1. Compare all trees in a file necom eval compare trees.nwk

2. Compare trees between two files necom eval compare set1.nwk set2.nwk