ArticleAlgorithms for molecular biology : AMB2015
Estimating evolutionary distances between genomic sequences from spaced-word matches.
Article in Algorithms for molecular biology : AMB, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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28 citing papers in PubMed.
- A k-mer-based estimator of the substitution rate between repetitive sequences.Algorithms for molecular biology : AMB · 2026Article
- ReSkmer: modeling repeats allows k-mer-based alignment-free methods to calculate population genomic distances.Genome biology · 2026Article
- EvANI benchmarking workflow for evolutionary distance estimation.Briefings in bioinformatics · 2025Article
- Integrating sequence composition information into microbial diversity analyses with k-mer frequency counting.mSystems · 2025Article
- EvANI benchmarking workflow for evolutionary distance estimation.bioRxiv : the preprint server for biology · 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
- How to optimally sample a sequence for rapid analysis.Bioinformatics (Oxford, England) · 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
- App-SpaM: phylogenetic placement of short reads without sequence alignment.Bioinformatics advances · 2021Article
- Information Theory in Computational Biology: Where We Stand Today.Entropy (Basel, Switzerland) · 2020Article
- 'Multi-SpaM': a maximum-likelihood approach to phylogeny reconstruction using multiple spaced-word matches and quartet trees.NAR genomics and bioinformatics · 2020Article
- The number of k-mer matches between two DNA sequences as a function of k and applications to estimate phylogenetic distances.PloS one · 2020Article
- Specificity Analysis of Genome Based on Statistically Identical K-Words With Same Base Combination.IEEE open journal of engineering in medicine and biology · 2020Article
- Read-SpaM: assembly-free and alignment-free comparison of bacterial genomes with low sequencing coverage.BMC bioinformatics · 2019Article
- Long-read amplicon denoising.Nucleic acids research · 2019Article
- Benchmarking of alignment-free sequence comparison methods.Genome biology · 2019Article
- Alignment-free method for DNA sequence clustering using Fuzzy integral similarity.Scientific reports · 2019Article
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4 authors.
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Abstract
Alignment-free methods are increasingly used to calculate evolutionary distances between DNA and protein sequences as a basis of phylogeny reconstruction. Most of these methods, however, use heuristic distance functions that are not based on any explicit model of molecular evolution. Herein, we propose a simple estimator d N of the evolutionary distance between two DNA sequences that is calculated from the number N of (spaced) word matches between them. We show that this distance function is more accurate than other distance measures that are used by alignment-free methods. In addition, we calculate the variance of the normalized number N of (spaced) word matches. We show that the variance of N is smaller for spaced words than for contiguous words, and that the variance is further reduced if our spaced-words approach is used with multiple patterns of 'match positions' and 'don't care positions'. Our software is available online and as downloadable source code at: http://spaced.gobics.de/.
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