Machine Learning Enables Alignment-Free Distance Calculation and Phylogenetic Placement Using k-Mer Frequencies.

ABSTRACT: A key application of phylogenetics in ecological studies is identifying unknown sequences with respect to known ones. This goal can be formalised as assigning taxonomic labels or inserting sequences into a reference phylogenetic tree (phylogenetic placement). Much attention has been paid to the phylogenetic placement of short fragments used in amplicon sequencing or metagenomics. However, placing longer pieces of DNA, such as assembled genomes, contigs, or long reads, is less studied. Placing long sequences should be easier than short reads due to their increased signal. However, handling larger inputs poses its own challenges including finding homologues and the computational burden. Here, we explore a phylogenetic placement method that uses k-mer frequencies to measure distances between

SUBMITTER: Rachtman E 

PROVIDER: S-EPMC12550494 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature