Specification: Phylogenetic Trees (OSCAR v1.0-v1.5)

Profiles: OSCAR v1.0, OSCAR v1.1, OSCAR v1.2, OSCAR v1.3, OSCAR v1.4, OSCAR v1.5 Other versions: Phylogenetic Trees (OSCAR v1.6-v1.8)

In OSCAR v1.0 through v1.5, phylogenetic trees are serialized with a bare root type name and the underlying polymake object directly as the data payload.

Encoding Notes

• Use _type: "PhylogeneticTree" at the root.
• Store the polymake tree object directly under data.
• Preserve the embedded polymake namespace and type information inside that payload.

Canonical Example Payload

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

{
  "_ns": {"Oscar": ["https://github.com/oscar-system/Oscar.jl", "1.5.1"]},
  "_type": "PhylogeneticTree",
  "data": {
    "LEAVES": {"B": 5, "C": 4, "G": 6, "H": 2},
    "_ns": {"polymake": ["https://polymake.org", "4.15"]},
    "EDGE_LENGTHS": [1, 3, 2, 1, 1, 4],
    "_type": "graph::PhylogeneticTree<Float>",
    "LABELS": ["", "", "H", "", "C", "B", "G"],
    "NEWICK": "((H:3,(C:1,B:1):2):1,G:4);",
    "ADJACENCY": [[1, 6], [0, 2, 3], [1], [1, 4, 5], [3], [3], [0]]
  }
}

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)