{
  "abstract": "Background: Reproducible taxonomic collapsing and geological-timescale annotation of time-calibrated phylogenetic trees in R often require coordination among several packages and repeated code for label parsing, clade validation, plotting, and export. Workflow-managed analyses additionally benefit from non-interactive configuration, predictable diagnostics, and machine-readable exit status. Results: We present Rclade, an R package that consolidates the multi-package coordination required for taxonomic collapsing into a streamlined, single-function interface. Rclade provides (1) custom ggproto objects (GeomPolygonStraight/GeomSegmentStraight) that bypass coord_munch() interpolation to achieve straight-edge rendering of collapsed triangles in circular layouts; (2) automatic detection and parsing of four taxonomic-label formats (GTDB, Silva, NCBI, embedded) plus user-supplied custom regex, with explicit input-validation contracts and parsing-accuracy evaluation on real and derived test sets; and (3) workflow embeddability through YAML configuration, library-mode APIs, and standard Unix exit codes. Benchmarks on synthetic and real datasets (200-10,000 synthetic tips and real reference trees up to 10,122 tips; 5 replicates at every scale under a unified fully rendered measurement protocol) show that the full-pipeline overhead is modest for interactive use (median {approx}0.87 s in-session rendering and {approx}8.4 s process-level wall-clock at 10,000 tips). Conclusions: Rclade is a convenience layer over the ggtree/deeptime ecosystem that reduces boilerplate while adding targeted technical improvements for circular-layout rendering and format heterogeneity management.",
  "abstract_shown": true,
  "affiliations": [
    "Shanghai Jiao Tong University"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 2,
  "authors": [
    {
      "name": "Z. Zeng"
    },
    {
      "affs": [
        0
      ],
      "name": "Y. Wang"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/7z3xjpc2dsax1.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.08.27.747462",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.08.27.747462v1.full",
  "id": "7z3xjpc2dsax1",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.08.27.747462v1",
  "language": null,
  "licence": "CC-BY-NC-ND",
  "licence_label": "CC BY-NC-ND",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "bioinformatics"
    ],
    [
      "openalex",
      "1312|Genomics and Phylogenetic Studies"
    ]
  ],
  "openalex": "W7204865949",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.08.27.747462v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-08-27",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/7z3xjpc2dsax1.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:18:19Z",
      "native_id": "10.64898/2026.08.27.747462",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.08.27.747462v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:bioinformatics",
      "subfield": "bioinformatics"
    }
  ],
  "title": "Rclade: automated taxonomic collapsing and geological-timescale annotation of time-calibrated phylogenetic trees in R",
  "title_text": "Rclade: automated taxonomic collapsing and geological-timescale annotation of time-calibrated phylogenetic trees in R",
  "type": "preprint",
  "updated_at": "2026-10-30T12:18:19Z",
  "url": "https://research.draconitic.com/paper/7z3xjpc2dsax1",
  "venue": "bioRxiv",
  "versions": []
}