Ksak: A high-throughput tool for alignment-free phylogenetics

Article Biochemical Research Methods

The power of word-frequency-based alignment-free functions: a comprehensive large-scale experimental analysis

Giuseppe Cattaneo et al.

Summary: The study focused on a representative set of word-frequency-based AF functions, providing a comprehensive evaluation of their power and Type I error. Results offered novel and informative characterizations of these AF functions, aiding in the selection of functions suitable for analysis tasks.

BIOINFORMATICS (2022)

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Article Multidisciplinary Sciences

Large-scale k-mer-based analysis of the informational properties of genomes, comparative genomics and taxonomy

Yuval Bussi et al.

Summary: Information theoretic approaches are commonly used in bioinformatics, particularly in comparative genomics where alignment-free methods using short DNA words (k-mers) are powerful. An analysis of 5805 genomes revealed that 21-mer and 31-mer Jaccard similarities can accurately recapitulate the phylogenetic tree of life, emphasizing the importance of whole-genome similarity for taxonomic classifications.

PLOS ONE (2021)

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Article Biotechnology & Applied Microbiology

Exploring short k-mer profiles in cells and mobile elements from Archaea highlights the major influence of both the ecological niche and evolutionary history

Ariane Bize et al.

Summary: K-mer-based methods have been greatly advanced in biological research, especially in the study of archaea and their mobilome. The 5-mer DNA profiles provide insights into the classification of archaea, the influence of environmental constraints, and the coevolution between mobile elements and hosts, which present specific patterns in the 5-mer profile.

BMC GENOMICS (2021)

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Article Biotechnology & Applied Microbiology