Specification: Phylogenetic Trees (OSCAR v1.6-v1.8)

Profiles: OSCAR v1.6, OSCAR v1.7, OSCAR v1.8 Other versions: Phylogenetic Trees (OSCAR v1.0-v1.5)

From OSCAR v1.6 onward, PhylogeneticTree uses a parametric root type and a structured payload that separates the polymake tree from additional OSCAR-level data such as vertex permutations.

Encoding Notes

• Use a typed _type object whose name is "PhylogeneticTree".
• Record the coefficient field in _type.params.
• Store the tree data under data, with at least pm_tree and any additional OSCAR-specific fields required by the profile.

Canonical Example Payload

The following payload is taken directly from the current rosetta-stone corpus.

{
  "_ns": {"Oscar": ["https://github.com/oscar-system/Oscar.jl", "1.7.0"]},
  "_type": {"name": "PhylogeneticTree", "params": {"_type": "Floats"}},
  "data": {
    "pm_tree": {
      "LEAVES": {"B": 5, "C": 4, "G": 6, "H": 2},
      "_type": "graph::PhylogeneticTree<Float>",
      "_ns": {"polymake": ["https://polymake.org", "4.15"]},
      "NEWICK": "((H:3,(C:1,B:1):2):1,G:4);",
      "N_NODES": 7,
      "LABELS": ["", "", "H", "", "C", "B", "G"],
      "ADJACENCY": [[1, 6], [0, 2, 3], [1], [1, 4, 5], [3], [3], [0]],
      "EDGE_LENGTHS": [1, 3, 2, 1, 1, 4]
    },
    "vertex_perm": ["1", "2", "3", "4", "5", "6", "7"]
  }
}

Documented Profiles in This Corpus

This table records the profile/version pairs currently represented by the rosetta-stone examples for this data type. Add new rows as new systems or encoding revisions are documented.

Rosetta Stone Examples

• Phylogenetic tree (Float64)
• Phylogenetic tree (QQ)