On the transformation of MinHash-based uncorrected distances into proper evolutionary distances for phylogenetic inference

Alexis Criscuolo (1, 2)

1 IP - Institut Pasteur [Paris]
2 Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB

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.

Mots clés: MinHash; p-distance; evolutionary distance; substitution model; phylogenetics; genome; simulation

Domaines: Bio-informatique [q-bio.QM]

Alexis Criscuolo. On the transformation of MinHash-based uncorrected distances into proper evolutionary distances for phylogenetic inference. F1000Research, 2020, 9, pp.1309. ⟨10.12688/f1000research.26930.1⟩. ⟨pasteur-03264539⟩