Insertions and deletions as phylogenetic signal in an alignment-free context.

ABSTRACT: Most methods for phylogenetic tree reconstruction are based on sequence alignments; they infer phylogenies from substitutions that may have occurred at the aligned sequence positions. Gaps in alignments are usually not employed as phylogenetic signal. In this paper, we explore an alignment-free approach that uses insertions and deletions (indels) as an additional source of information for phylogeny inference. For a set of four or more input sequences, we generate so-called quartet blocks of four putative homologous segments each. For pairs of such quartet blocks involving the same four sequences, we compare the distances between the two blocks in these sequences, to obtain hints about indels that may have happened between the blocks since the respective four sequences have evolved from the

SUBMITTER: Birth N 

PROVIDER: S-EPMC9387925 | biostudies-literature | 2022 Aug

REPOSITORIES: biostudies-literature