{
  "abstract": "Whole-genome alignment (WGA) is widely used for genome-scale phylogenetic inference, and most scalable WGA pipelines rely on progressive alignment guided by a pre-specified tree. Among progressive whole-genome aligners, Progressive Cactus is a successful state-of-the-art method. However, analyses of real and simulated avian data indicate that guide-tree choice can influence downstream tree inference; star guide trees do not remove this effect and can exacerbate long-branch attraction artefacts. We have developed a consensus strategy based on the Progressive Cactus framework by generating a small set of alternative guide-tree alignments and retaining only homology relationships consistently recovered across all alignments. In simulation experiments, consensus alignments improve precision, bring inferred site-pattern frequency distributions closer to those of the true alignments, and recover more true splits than single guide-tree alignments. In a real landbird (Telluraves) dataset, we observe a strong bias towards single binary guide trees and long-branch attraction for less resolved trees. While the reconstructed tree still depends on the phylogenetic method and taxa sampling, our consensus alignment has no clear bias. We implemented a hierarchical consensus workflow that only locally resolves uncertainty in the guide tree. Therefore, the computational cost increases only moderately, for example by an estimated 68 percent for a recently published large-scale alignment of more than 300 modern birds (Neoaves) taxa.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 2,
  "authors": [
    {
      "name": "Q. Tao"
    },
    {
      "name": "S. Grünewald"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/d8p3nw620pf6v.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.07.06.736671",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.07.06.736671v2.full",
  "id": "d8p3nw620pf6v",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.07.06.736671v2",
  "language": null,
  "licence": "CC-BY-NC",
  "licence_label": "CC BY-NC",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "evolutionary biology"
    ],
    [
      "openalex",
      "1312|Genomics and Phylogenetic Studies"
    ]
  ],
  "openalex": "W7167802176",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.07.06.736671v2.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-07-06",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/d8p3nw620pf6v.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:24:15Z",
      "native_id": "10.64898/2026.07.06.736671",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.07.06.736671v3"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:evolutionary biology",
      "subfield": "evolutionary-biology"
    }
  ],
  "title": "Guide-tree bias of whole genome alignment can mislead phylogenomic analyses",
  "title_text": "Guide-tree bias of whole genome alignment can mislead phylogenomic analyses",
  "type": "preprint",
  "updated_at": "2026-11-04T00:21:01Z",
  "url": "https://research.draconitic.com/paper/d8p3nw620pf6v",
  "venue": "bioRxiv",
  "versions": []
}