ArticleGenome biology2019
Benchmarking of alignment-free sequence comparison methods.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 105 papers.
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Who cites it
105 citing papers in PubMed.
- CAKR: commutative algebra k-mer representations for genomics.Nature communications · 2026Article
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- Reference-free clustering as an epidemiological tool forMicrobial genomics · 2026Article
- ReSkmer: modeling repeats allows k-mer-based alignment-free methods to calculate population genomic distances.Genome biology · 2026Article
- Hash functions in nucleotide sequence analysis.Genome research · 2026Review
- Article
- MosaicLev: modified Levenshtein distance for mobile element-aware genome comparison.Bioinformatics advances · 2026Article
- Estimating Genome-Wide Phylogenies Using Probabilistic Topic Modeling.Systematic biology · 2025Article
- Machine Learning Enables Alignment-Free Distance Calculation and Phylogenetic Placement Using k-Mer Frequencies.Molecular ecology resources · 2025Article
- BioSet2Vec: extraction of k-mer dictionaries from multiple sets of biological sequences via big data technologies.BMC bioinformatics · 2025Article
- Comparative analysis of RAD-seq methods for SNP discovery and genetic diversity assessment in oil seed crop safflower.Scientific reports · 2025Article
- SEQSIM: A novel bioinformatics tool for comparisons of promoter regions-a case study of calcium binding protein spermatid associated 1 (CABS1).BMC bioinformatics · 2025Article
- Starship giant transposable elements cluster by host taxonomy using k-mer-based phylogenetics.G3 (Bethesda, Md.) · 2025Article
- Conservation of regulatory elements with highly diverged sequences across large evolutionary distances.Nature genetics · 2025Article
- Sequence similarity estimation by random subsequence sketching.bioRxiv : the preprint server for biology · 2025Article
- EvANI benchmarking workflow for evolutionary distance estimation.Briefings in bioinformatics · 2025Article
- Alignment-free viral sequence classification at scale.BMC genomics · 2025Article
- An alignment-free method for phylogeny estimation using maximum likelihood.BMC bioinformatics · 2025Article
- K-mer-based Approaches to Bridging Pangenomics and Population Genetics.Molecular biology and evolution · 2025Review
- GRAMEP: an alignment-free method based on the maximum entropy principle for identifying SNPs.BMC bioinformatics · 2025Article
45 more citing papers are in PubMed but not listed here.
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Authors and funding
19 authors.
Funding
Abstract
backgroundAlignment-free (AF) sequence comparison is attracting persistent interest driven by data-intensive applications. Hence, many AF procedures have been proposed in recent years, but a lack of a clearly defined benchmarking consensus hampers their performance assessment.
resultsHere, we present a community resource (http://afproject.org) to establish standards for comparing alignment-free approaches across different areas of sequence-based research. We characterize 74 AF methods available in 24 software tools for five research applications, namely, protein sequence classification, gene tree inference, regulatory element detection, genome-based phylogenetic inference, and reconstruction of species trees under horizontal gene transfer and recombination events.
conclusionThe interactive web service allows researchers to explore the performance of alignment-free tools relevant to their data types and analytical goals. It also allows method developers to assess their own algorithms and compare them with current state-of-the-art tools, accelerating the development of new, more accurate AF solutions.
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