ArticleF1000Research2020
On the transformation of MinHash-based uncorrected distances into proper evolutionary distances for phylogenetic inference.
Article in F1000Research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed.
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- Rathayibacter tanaceti sp. nov., a Novel Actinobacterium from Tanacetum vulgare Infested by Foliar Nematode Aphelenchoides sp.Current microbiology · 2024Article
- Mottle: Accurate pairwise substitution distance at high divergence through the exploitation of short-read mappers and gradient descent.PloS one · 2024Article
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- Paenibacillus plantiphilus sp. nov. from the plant environment of Zea mays.Antonie van Leeuwenhoek · 2023Article
- Genomic sketching with multiplicities and locality-sensitive hashing using Dashing 2.Genome research · 2023Article
- RabbitTClust: enabling fast clustering analysis of millions of bacteria genomes with MinHash sketches.Genome biology · 2023Article
- Distribution of Bacterial Endosymbionts of theInternational journal of molecular sciences · 2023Article
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- Paenibacillus allorhizoplanae sp. nov. from the rhizoplane of a Zea mays root.Archives of microbiology · 2022Article
- A Dual Barcoding Approach to Bacterial Strain Nomenclature: Genomic Taxonomy of Klebsiella pneumoniae Strains.Molecular biology and evolution · 2022Article
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Abstract
Recently developed MinHash-based techniques were proven successful in quickly estimating the level of similarity between large nucleotide sequences. This article discusses their usage and limitations in practice to approximating uncorrected distances between genomes, and transforming these pairwise dissimilarities into proper evolutionary distances. It is notably shown that complex distance measures can be easily approximated using simple transformation formulae based on few parameters. MinHash-based techniques can therefore be very useful for implementing fast yet accurate alignment-free phylogenetic reconstruction procedures from large sets of genomes. This last point of view is assessed with a simulation study using a dedicated bioinformatics tool.
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