HIPSTR: highest independent posterior subtree reconstruction in TreeAnnotator X.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40924543", "kind": "science-record", "revision": 2, "content_hash": "sha256:8403ed9180aff622727a14a3fce1175df252cde1c1cc917858a32ece84a8e54a", "created_at": "2026-11-01T20:31:01Z", "updated_at": "2026-11-01T21:35:45Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "HIPSTR: highest independent posterior subtree reconstruction in TreeAnnotator X.", "doi": "10.1093/bioinformatics/btaf488", "pmid": "40924543", "authors": ["Guy Baele", "Luiz M Carvalho", "Marius Brusselmans", "Gytis Dudas", "Xiang Ji", "John T McCrone", "Philippe Lemey", "Marc A Suchard", "Andrew Rambaut"], "journal": "Bioinformatics (Oxford, England)", "year": 2025, "abstract": "SUMMARY: In Bayesian phylogenetic and phylodynamic studies, it is common to summarize the posterior distribution of trees with a time-calibrated summary phylogeny. While the maximum clade credibility (MCC) tree is often used for this purpose, we here show that a novel summary tree method-the highest independent posterior subtree reconstruction, or (HIPSTR)-contains consistently higher supported clades over MCC. We also provide faster computational routines for estimating both summary trees in an updated version of TreeAnnotator X, an open-source software program that summarizes the information from a sample of trees and returns many helpful statistics such as individual clade credibilities contained in the summary tree.\nRESULTS: HIPSTR and MCC reconstructions on two Ebola virus and two SARS-CoV-2 datasets show that HIPSTR yields summary trees that consistently contain clades with higher support compared to MCC trees. The MCC trees regularly fail to include several clades with very high posterior probability (≥0.95) as well as a large number of clades with moderate to high posterior probability (≥50%), whereas HIPSTR-in particular its majority-rule extension MrHIPSTR-achieves near-perfect performance in this respect. HIPSTR and MrHIPSTR also exhibit favourable computational performance over MCC in TreeAnnotator X. Comparison to the recent CCD0-MAP algorithm yielded mixed results and requires a more in-depth investigation in follow-up studies.\nAVAILABILITY AND IMPLEMENTATION: TreeAnnotator X is available as part of the BEAST X (v10.5.0) software package, available at https://github.com/beast-dev/beast-mcmc/releases, and on Zenodo (DOI: https://doi.org/10.5281/zenodo.4895234).", "claims": [{"id": "claim-method", "statement": "We here propose a summary tree approach—the highest independent posterior subtree reconstruction (HIPSTR) algorithm—that attempts to address the limitations of both majority-rule consensus trees and MCC trees.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40924543", "locator": "sections[1] \"1 Introduction\" paragraph 7", "quote": "We here propose a summary tree approach—the highest independent posterior subtree reconstruction (HIPSTR) algorithm—that attempts to address the limitations of both majority-rule consensus trees and MCC trees."}], "state": "complete"}, {"id": "claim-data-access", "statement": "No new data were generated or analysed in support of this research.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40924543", "locator": "sections[12] \"Data availability\" paragraph 2", "quote": "No new data were generated or analysed in support of this research."}], "state": "complete"}, {"id": "claim-target-result", "statement": "HIPSTR consistently yields summary trees with higher log marginal clade credibility and mean individual clade credibility over MCC trees, while doing so in a markedly shorter time compared to the MCC algorithm.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40924543", "locator": "sections[6] \"3 Results\" paragraph 2", "quote": "HIPSTR consistently yields summary trees with higher log marginal clade credibility and mean individual clade credibility over MCC trees, while doing so in a markedly shorter time compared to the MCC algorithm."}, {"asset": "source:pmid:40924543", "locator": "sections[6] \"3 Results\" paragraph 4", "quote": "On the datasets tested HIPSTR and MrHIPSTR perform up to 2× faster than MCC."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "HIPSTR consistently yields summary trees with higher log marginal clade credibility and mean individual clade credibility over MCC trees, while doing so in a markedly shorter time compared to the MCC algorithm.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:40924543"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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