Gardes J, Maldivi C, Boisset D, Aubourg T, Demongeot J. An Unsupervised Classifier for Whole-Genome Phylogenies, the Maxwell© Tool.
Int J Mol Sci 2023;
24:16278. [PMID:
38003468 PMCID:
PMC10671764 DOI:
10.3390/ijms242216278]
[Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/20/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
The development of phylogenetic trees based on RNA or DNA sequences generally requires a precise and limited choice of important RNAs, e.g., messenger RNAs of essential proteins or ribosomal RNAs (like 16S), but rarely complete genomes, making it possible to explain evolution and speciation. In this article, we propose revisiting a classic phylogeny of archaea from only the information on the succession of nucleotides of their entire genome. For this purpose, we use a new tool, the unsupervised classifier Maxwell, whose principle lies in the Burrows-Wheeler compression transform, and we show its efficiency in clustering whole archaeal genomes.
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