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oai:riuma.uma.es:10630/401432026-02-03T11:34:35Zcom_10630_2254col_10630_37953

Aledo-Ramos, Juan Carlos 2025-10-09T06:58:52Z 2025-10-09T06:58:52Z 2022-05-06 Aledo, J.C. Phylogenies from unaligned proteomes using sequence environments of amino acid residues. Sci Rep 12, 7497 (2022). https://doi.org/10.1038/s41598-022-11370-x https://hdl.handle.net/10630/40143 10.1038/s41598-022-11370-x Alignment-free methods for sequence comparison and phylogeny inference have attracted a great deal of attention in recent years. Several algorithms have been implemented in diverse software packages. Despite the great number of existing methods, most of them are based on word statistics. Although they propose different filtering and weighting strategies and explore different metrics, their performance may be limited by the phylogenetic signal preserved in these words. Herein, we present a different approach based on the species-specific amino acid neighborhood preferences. These differential preferences can be assessed in the context of vector spaces. In this way, a distance-based method to build phylogenies has been developed and implemented into an easy-to-use R package. Tests run on real-world datasets show that this method can reconstruct phylogenetic relationships with high accuracy, and often outperforms other alignment-free approaches. Furthermore, we present evidence that the new method can perform reliably on datasets formed by non-orthologous protein sequences, that is, the method not only does not require the identification of orthologous proteins, but also does not require their presence in the analyzed dataset. These results suggest that the neighborhood preference of amino acids conveys a phylogenetic signal that may be of great utility in phylogenomics. eng http://creativecommons.org/licenses/by/4.0/ open access Attribution 4.0 Internacional Filogenia Proteómica Bioinformática Phylogenies from unaligned proteomes using sequence environments of amino acid residues. journal article