ArticleBioinformatics (Oxford, England)2020
Phylonium: fast estimation of evolutionary distances from large samples of similar genomes.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
- Seqwin: Ultrafast identification of signature sequences in microbial genomes.bioRxiv : the preprint server for biology · 2025Article
- A multi-isolate genomic approach identifies diverseMicrobial genomics · 2025Article
- SANS ambages: phylogenomics with abundance-filter, multi-threading, and bootstrapping on amino-acid or genomic sequences.BMC bioinformatics · 2025Article
- An alignment-free method for phylogeny estimation using maximum likelihood.BMC bioinformatics · 2025Article
- CGRclust: Chaos Game Representation for twin contrastive clustering of unlabelled DNA sequences.BMC genomics · 2024Article
- Capturing clinically relevantMicrobial genomics · 2024Article
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- Marker discovery in the large.Bioinformatics advances · 2024Article
- Mottle: Accurate pairwise substitution distance at high divergence through the exploitation of short-read mappers and gradient descent.PloS one · 2024Article
- CoreDetector: a flexible and efficient program for core-genome alignment of evolutionary diverse genomes.Bioinformatics (Oxford, England) · 2023Article
- Populational genomic insights ofFrontiers in microbiology · 2023Article
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- A global pangenome for the wheat fungal pathogenMicrobial genomics · 2022Article
- Fur: Find unique genomic regions for diagnostic PCR.Bioinformatics (Oxford, England) · 2021Article
- Article
- On the transformation of MinHash-based uncorrected distances into proper evolutionary distances for phylogenetic inference.F1000Research · 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
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2 authors.
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Abstract
motivationTracking disease outbreaks by whole-genome sequencing leads to the collection of large samples of closely related sequences. Five years ago, we published a method to accurately compute all pairwise distances for such samples by indexing each sequence. Since indexing is slow, we now ask whether it is possible to achieve similar accuracy when indexing only a single sequence.
resultsWe have implemented this idea in the program phylonium and show that it is as accurate as its predecessor and roughly 100 times faster when applied to all 2678 Escherichia coli genomes contained in ENSEMBL. One of the best published programs for rapidly computing pairwise distances, mash, analyzes the same dataset four times faster but, with default settings, it is less accurate than phylonium. AVAILABILITY AND IMPLEMENTATION: Phylonium runs under the UNIX command line; its C++ sources and documentation are available from github.com/evolbioinf/phylonium. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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