ArticleBMC bioinformatics2019
Read-SpaM: assembly-free and alignment-free comparison of bacterial genomes with low sequencing coverage.
Article in BMC bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed, 31 citations in OpenAlex.
- Machine Learning Enables Alignment-Free Distance Calculation and Phylogenetic Placement Using k-Mer Frequencies.Molecular ecology resources · 2025Article
- An alignment-free method for phylogeny estimation using maximum likelihood.BMC bioinformatics · 2025Article
- SHARK enables sensitive detection of evolutionary homologs and functional analogs in unalignable and disordered sequences.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- CONSULT-II: accurate taxonomic identification and profiling using locality-sensitive hashing.Bioinformatics (Oxford, England) · 2024Article
- Quantifying the uncertainty of assembly-free genome-wide distance estimates and phylogenetic relationships using subsampling.Cell systems · 2022Article
- Insertions and deletions as phylogenetic signal in an alignment-free context.PLoS computational biology · 2022Article
- Genome-wide alignment-free phylogenetic distance estimation under a no strand-bias model.Bioinformatics advances · 2022Article
- CONSULT: accurate contamination removal using locality-sensitive hashing.NAR genomics and bioinformatics · 2021Article
- High-Throughput Genomic Data Reveal Complex Phylogenetic Relationships inFrontiers in genetics · 2021Article
- App-SpaM: phylogenetic placement of short reads without sequence alignment.Bioinformatics advances · 2021Article
- Efficient DNA sequence compression with neural networks.GigaScience · 2020Article
- Beyond DNA barcoding: The unrealized potential of genome skim data in sample identification.Molecular ecology · 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
- Benchmarking of alignment-free sequence comparison methods.Genome biology · 2019Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIn many fields of biomedical research, it is important to estimate phylogenetic distances between taxa based on low-coverage sequencing reads. Major applications are, for example, phylogeny reconstruction, species identification from small sequencing samples, or bacterial strain typing in medical diagnostics.
resultsWe adapted our previously developed software program Filtered Spaced-Word Matches (FSWM) for alignment-free phylogeny reconstruction to take unassembled reads as input; we call this implementation Read-SpaM.
conclusionsTest runs on simulated reads from semi-artificial and real-world bacterial genomes show that our approach can estimate phylogenetic distances with high accuracy, even for large evolutionary distances and for very low sequencing coverage.
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