Guide-tree bias of whole genome alignment can mislead phylogenomic analyses
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.
Related
- Reference mapping and whole-genome alignment yield comparable phylogenomic inferences
- Whole-Genome sequencing and phylogenomic analyses of Alternaria japonica and A . telliensis (Section Japonicae )
- Anvaya: phylogenomic analysis of chromosome fusion-and-mixing characters and detection of shared whole-genome duplication
- Genome-wide analyses resolve three clonal lineages and lineage-specific ploidy in Phytophthora cinnamomi
- A Distinct Mode of Chromosome-End Genome Instability Revealed by Circulome Characterization and Analyses
BibTeX
@misc{tao2026guidetree,
title = {{Guide-tree bias of whole genome alignment can mislead phylogenomic analyses}},
author = {Q. Tao and S. Grünewald},
howpublished = {bioRxiv},
year = {2026},
month = jul,
doi = {10.64898/2026.07.06.736671},
url = {https://www.biorxiv.org/content/10.64898/2026.07.06.736671v2},
note = {CC BY-NC},
}
RIS
TY - UNPB
TI - Guide-tree bias of whole genome alignment can mislead phylogenomic analyses
AU - Q. Tao
AU - S. Grünewald
PY - 2026
DA - 2026/07/06
PB - bioRxiv
DO - 10.64898/2026.07.06.736671
UR - https://www.biorxiv.org/content/10.64898/2026.07.06.736671v2
AB - 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.
ER -