ArticlePloS one2020
The number of k-mer matches between two DNA sequences as a function of k and applications to estimate phylogenetic distances.
Article in PloS one, 2020. 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.
- Estimation of substitution and indel rates via k-mer statistics.Algorithms for molecular biology : AMB · 2026Article
- A k-mer-based estimator of the substitution rate between repetitive sequences.Algorithms for molecular biology : AMB · 2026Article
- Estimation of substitution and indel rates viaAlgorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop) · 2025Article
- Estimation of substitution and indel rates viabioRxiv : the preprint server for biology · 2025Article
- An alignment-free method for phylogeny estimation using maximum likelihood.BMC bioinformatics · 2025Article
- A k-mer-Based Estimator of the Substitution Rate Between Repetitive Sequences.Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop) · 2025Article
- A survey of k-mer methods and applications in bioinformatics.Computational and structural biotechnology journal · 2024Review
- The Statistics of Parametrized Syncmers in a Simple Mutation Process Without Spurious Matches.Journal of computational biology : a journal of computational molecular cell biology · 2024Article
- Mottle: Accurate pairwise substitution distance at high divergence through the exploitation of short-read mappers and gradient descent.PloS one · 2024Article
- Genome assembly composition of the String "ACGT" array: a review of data structure accuracy and performance challenges.PeerJ. Computer science · 2023Article
- Insertions and deletions as phylogenetic signal in an alignment-free context.PLoS computational biology · 2022Article
- The Statistics ofJournal of computational biology : a journal of computational molecular cell biology · 2022Article
- Genome-wide alignment-free phylogenetic distance estimation under a no strand-bias model.Bioinformatics advances · 2022Article
- Article
- Sequence Comparison Without Alignment: The SpaM Approaches.Methods in molecular biology (Clifton, N.J.) · 2021Article
- App-SpaM: phylogenetic placement of short reads without sequence alignment.Bioinformatics advances · 2021Article
- Phylonium: fast estimation of evolutionary distances from large samples of similar genomes.Bioinformatics (Oxford, England) · 2020Article
- 'Multi-SpaM': a maximum-likelihood approach to phylogeny reconstruction using multiple spaced-word matches and quartet trees.NAR genomics and bioinformatics · 2020Article
- On the transformation of MinHash-based uncorrected distances into proper evolutionary distances for phylogenetic inference.F1000Research · 2020Article
- Read-SpaM: assembly-free and alignment-free comparison of bacterial genomes with low sequencing coverage.BMC bioinformatics · 2019Article
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6 authors.
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Abstract
We study the number Nk of length-k word matches between pairs of evolutionarily related DNA sequences, as a function of k. We show that the Jukes-Cantor distance between two genome sequences-i.e. the number of substitutions per site that occurred since they evolved from their last common ancestor-can be estimated from the slope of a function F that depends on Nk and that is affine-linear within a certain range of k. Integers kmin and kmax can be calculated depending on the length of the input sequences, such that the slope of F in the relevant range can be estimated from the values F(kmin) and F(kmax). This approach can be generalized to so-called Spaced-word Matches (SpaM), where mismatches are allowed at positions specified by a user-defined binary pattern. Based on these theoretical results, we implemented a prototype software program for alignment-free sequence comparison called Slope-SpaM. Test runs on real and simulated sequence data show that Slope-SpaM can accurately estimate phylogenetic distances for distances up to around 0.5 substitutions per position. The statistical stability of our results is improved if spaced words are used instead of contiguous words. Unlike previous alignment-free methods that are based on the number of (spaced) word matches, Slope-SpaM produces accurate results, even if sequences share only local homologies.
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