ArticleNature methods2025
Efficient and robust search of microbial genomes via phylogenetic compression.
Article in Nature methods, 2025. 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.
- Genomic and phenotypic characterization of Klebsiella pneumoniae phage KP Ø1: a novel lytic Slopekvirus targeting uropathogenic multidrug-resistant Klebsiella pneumoniae.Scientific reports · 2026Article
- Efficient sequence alignment against millions of prokaryotic genomes with LexicMap.Nature biotechnology · 2026Article
- New algorithm enables fast 'gold-standard' search of the world's largest microbial DNA archives.Nature biotechnology · 2026Article
- AllTheBacteria: a community resource empowers biology and discovers novel peptide antibiotics.bioRxiv : the preprint server for biology · 2026Article
- Leveraging microbial phylogeny for computational efficiency.Nature reviews. Microbiology · 2026Article
- Strain-level metagenomic profiling using pangenome graphs with PanTax.Genome research · 2026Article
- Compressive pangenomics using mutation-annotated networks.Nature genetics · 2026Article
- MBGC2: Boosting compression via efficient encoding of approximate matches in genome collections.GigaScience · 2026Article
- Novel genes arise from genomic deletions across the bacterial tree of life.bioRxiv : the preprint server for biology · 2026Article
- FroM Superstring to Indexing: a space-efficient index for unconstrainedBioinformatics advances · 2026Article
- Article
- CREMSA: compressed indexing of (ultra) large multiple sequence alignments.Bioinformatics (Oxford, England) · 2025Article
- BWT construction and search at the terabase scale.Bioinformatics (Oxford, England) · 2024Article
- Seamless, rapid, and accurate analyses of outbreak genomic data using splitGenome research · 2024Article
- Where the Patterns Are: Repetition-Aware Compression for Colored de Bruijn GraphsJournal of computational biology : a journal of computational molecular cell biology · 2024Article
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Abstract
Comprehensive collections approaching millions of sequenced genomes have become central information sources in the life sciences. However, the rapid growth of these collections has made it effectively impossible to search these data using tools such as the Basic Local Alignment Search Tool (BLAST) and its successors. Here, we present a technique called phylogenetic compression, which uses evolutionary history to guide compression and efficiently search large collections of microbial genomes using existing algorithms and data structures. We show that, when applied to modern diverse collections approaching millions of genomes, lossless phylogenetic compression improves the compression ratios of assemblies, de Bruijn graphs and k-mer indexes by one to two orders of magnitude. Additionally, we develop a pipeline for a BLAST-like search over these phylogeny-compressed reference data, and demonstrate it can align genes, plasmids or entire sequencing experiments against all sequenced bacteria until 2019 on ordinary desktop computers within a few hours. Phylogenetic compression has broad applications in computational biology and may provide a fundamental design principle for future genomics infrastructure.
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