Genome-wide alignment-free phylogenetic distance estimation under a no strand-bias model.

ABSTRACT: While alignment has been the dominant approach for determining homology prior to phylogenetic inference, alignment-free methods can simplify the analysis, especially when analyzing genome-wide data. Furthermore, alignment-free methods present the only option for emerging forms of data, such as genome skims, which do not permit assembly. Despite the appeal, alignment-free methods have not been competitive with alignment-based methods in terms of accuracy. One limitation of alignment-free methods is their reliance on simplified models of sequence evolution such as Jukes-Cantor. If we can estimate frequencies of base substitutions in an alignment-free setting, we can compute pairwise distances under more complex models. However, since the strand of DNA sequences is unknown for many forms of g

SUBMITTER: Balaban M 

PROVIDER: S-EPMC9383262 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature