Phylogenies from unaligned proteomes using sequence environments of amino acid residues.

ABSTRACT: 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 rea

SUBMITTER: Aledo JC 

PROVIDER: S-EPMC9076898 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature