ArticleCell systems2022
Quantifying the uncertainty of assembly-free genome-wide distance estimates and phylogenetic relationships using subsampling.
Article in Cell systems, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 12 citations in OpenAlex.
- DipSkmer: Reference-free population genomics with diploid genome skims.bioRxiv : the preprint server for biology · 2026Article
- Machine Learning Enables Alignment-Free Distance Calculation and Phylogenetic Placement Using k-Mer Frequencies.Molecular ecology resources · 2025Article
- Rapid species-level metagenome profiling and containment estimation with sylph.Nature biotechnology · 2025Article
- Article
- Scaling DEPP phylogenetic placement to ultra-large reference trees: a tree-aware ensemble approach.Bioinformatics (Oxford, England) · 2024Article
- DEPP: Deep Learning Enables Extending Species Trees using Single Genes.Systematic biology · 2023Article
- Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Computing distance between two genomes without alignments or even access to assemblies has many downstream analyses. However, alignment-free methods, including in the fast-growing field of genome skimming, are hampered by a significant methodological gap. While accurate methods (many k-mer-based) for assembly-free distance calculation exist, measuring the uncertainty of estimated distances has not been sufficiently studied. In this paper, we show that bootstrapping, the standard non-parametric method of measuring estimator uncertainty, is not accurate for k-mer-based methods that rely on k-mer frequency profiles. Instead, we propose using subsampling (with no replacement) in combination with a correction step to reduce the variance of the inferred distribution. We show that the distribution of distances using our procedure matches the true uncertainty of the estimator. The resulting phylogenetic support values effectively differentiate between correct and incorrect branches and identify controversial branches that change across alignment-free and alignment-based phylogenies reported in the literature.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.