{
  "annotation_id": "abfab0ba-fdb8-4228-a387-cc61b72227ed",
  "date_created": "2026-03-02T18:01:32.292000Z",
  "date_modified": "2026-03-02T18:01:32.292000Z",
  "file_hash": "b4926bb4c858c4733a905d3aec83719e544b3e5931367833c1f78c7c5aa6d948",
  "private": false,
  "record": {
    "abstract": "We introduce a Markov model for the evolution of a gene family along a\nphylogeny. The model includes parameters for the rates of horizontal gene\ntransfer, gene duplication, and gene loss, in addition to branch lengths in the\nphylogeny. The likelihood for the changes in the size of a gene family across\ndifferent organisms can be calculated in O(N+hM^2) time and O(N+M^2) space,\nwhere N is the number of organisms, $h$ is the height of the phylogeny, and M\nis the sum of family sizes. We apply the model to the evolution of gene content\nin Preoteobacteria using the gene families in the COG (Clusters of Orthologous\nGroups) database.",
    "arxiv_id": "q-bio/0509037",
    "authors": [
      "Mikl\u00f3s Cs\u0171r\u00f6s",
      "Istv\u00e1n Mikl\u00f3s"
    ],
    "categories": [
      "q-bio.PE",
      "q-bio.QM"
    ],
    "doi": "10.1007/11732990_18",
    "title": "A probabilistic model for gene content evolution with duplication, loss,   and horizontal transfer",
    "url": "https://arxiv.org/abs/q-bio/0509037"
  },
  "schema_id": "dorsal/arxiv",
  "source": {
    "execution_id": "e04d9e87-ec79-48be-8cbb-521744af215d",
    "id": "arXiv Dataset IDs",
    "type": "Model",
    "variant": "snapshot-2026-03-01",
    "version": "0.1.0"
  },
  "user_id": 1000002
}