An alignment-free method for phylogeny estimation using maximum likelihood.

ABSTRACT:

Background

While alignment has traditionally been the primary approach for establishing homology prior to phylogenetic inference, alignment-free methods offer a simplified alternative, particularly beneficial when handling genome-wide data involving long sequences and complex events such as rearrangements. Moreover, alignment-free methods become crucial for data types like genome skims, where assembly is impractical. However, despite these benefits, alignment-free techniques have not gained widespread acceptance since they lack the accuracy of alignment-based techniques, primarily due to their reliance on simplified models of pairwise distance calculation.

Results

Here, we present a likelihood based alignment-free technique for phylogenetic tree construction. We encode the p

SUBMITTER: Zahin T 

PROVIDER: S-EPMC11887328 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature