Ultrafast learning of four-node hybridization cycles in phylogenetic networks using algebraic invariants.

ABSTRACT:

Motivation

The abundance of gene flow in the Tree of Life challenges the notion that evolution can be represented with a fully bifurcating process which cannot capture important biological realities like hybridization, introgression, or horizontal gene transfer. Coalescent-based network methods are increasingly popular, yet not scalable for big data, because they need to perform a heuristic search in the space of networks as well as numerical optimization that can be NP-hard. Here, we introduce a novel method to reconstruct phylogenetic networks based on algebraic invariants. While there is a long tradition of using algebraic invariants in phylogenetics, our work is the first to define phylogenetic invariants on concordance factors (frequencies of four-taxon splits in the input gen

SUBMITTER: Wu Z 

PROVIDER: S-EPMC10879748 | biostudies-literature | 2024

REPOSITORIES: biostudies-literature