ReviewGenome biology2017
Alignment-free sequence comparison: benefits, applications, and tools.
Review in Genome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 236 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
236 citing papers in PubMed.
- Alignment-Free Genome Geometry and Mosaic Barcodes Characterize Modular Diversity in the Cacao Swollen Shoot Virus Complex.Viruses · 2026Article
- Alignment-freeJournal of clinical microbiology · 2026Article
- CAKR: commutative algebra k-mer representations for genomics.Nature communications · 2026Article
- Task geometry alignment enables parameter independent and accurate genomic search.Scientific reports · 2026Article
- MKMC enables reference-free transcriptomic analysis using k-mer representations.bioRxiv : the preprint server for biology · 2026Article
- Estimation of substitution and indel rates via k-mer statistics.Algorithms for molecular biology : AMB · 2026Article
- Evolving strategies for virus discovery.Microbial genomics · 2026Review
- The gift of novelty: repeat-robust k-mer-based estimators of mutation rates.Bioinformatics (Oxford, England) · 2026Article
- 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
- From atoms to fragments: a coarse representation for efficient and functional protein design.Bioinformatics (Oxford, England) · 2026Article
- The gift of novelty: repeat-robustbioRxiv : the preprint server for biology · 2026Article
- Ensemble Deep Learning Models on Raw DNA Sequences for Viral Genome Identification in Human Samples.Sensors (Basel, Switzerland) · 2026Article
- Alignment-Free Guided Design of a Pan-Orthoflavivirus RT-qPCR Assay.bioRxiv : the preprint server for biology · 2026Article
- GenCore: Genomic distance estimation using Locally Consistent Parsing.bioRxiv : the preprint server for biology · 2026Article
- MicrobialScope: an integrated genomic resource with rich annotations across bacteria, archaea, fungi, and viruses.Nucleic acids research · 2026Article
- Sequence based virus host prediction: a curated dataset and generalizable framework for training artificial intelligence to identify viruses of humans.Virus evolution · 2026Article
- Leveraging Different Distance Functions to Predict Antiviral Peptides with Geometric Deep Learning from ESMFold-Predicted Tertiary Structures.Antibiotics (Basel, Switzerland) · 2026Article
- Life at the extremes: maximally divergent microbes with similar genomic signatures linked to extreme environments.NAR genomics and bioinformatics · 2025Article
- Machine Learning Enables Alignment-Free Distance Calculation and Phylogenetic Placement Using k-Mer Frequencies.Molecular ecology resources · 2025Article
176 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of recombined sequences. The strength of these methods makes them particularly useful for next-generation sequencing data processing and analysis. However, many researchers are unclear about how these methods work, how they compare to alignment-based methods, and what their potential is for use for their research. We address these questions and provide a guide to the currently available alignment-free sequence analysis tools.
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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.