ArticleBioinformatics (Oxford, England)2025
HIPSTR: highest independent posterior subtree reconstruction in TreeAnnotator X.
Article in Bioinformatics (Oxford, England), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed.
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- Navigating the mysterious space of evolutionary histories.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Biological causes and impacts of rugged tree landscapes in phylodynamic inference.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Evolutionary history of Jamestown Canyon virus disentangles complex multi-vector ecology.bioRxiv : the preprint server for biology · 2026Article
- Characterizing the parvovirome of Swazi bats: novel species, highly divergent lineages, endogenous viral elements, and taxonomic challenges.Virus evolution · 2026Article
- Structural and phenotypic plasticity of the RBD loop2 region is a key determinant for HKU5r-CoVs' emergence in mink.bioRxiv : the preprint server for biology · 2025Article
- Mitogenomic Characterization ofBiology · 2025Article
- Circumpolar spread of avian influenza H5N1 to southern Indian Ocean islands.Nature communications · 2025Article
- Parallel algorithms for phylogenetic inference under a structured coalescent approximation.bioRxiv : the preprint server for biology · 2025Article
- Biological causes and impacts of rugged tree landscapes in phylodynamic inference.bioRxiv : the preprint server for biology · 2025Article
- Phylogenetics and Evolutionary Dynamics of Yunnan Acrididae Grasshoppers Inferred from 17 New Mitochondrial Genomes.Insects · 2025Article
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Abstract
summaryIn 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.
resultsHIPSTR 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. AVAILABILITY 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).
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