APOGeT: Automated Phylogeny over Geological Time-scales

TL;DR

APOGeT is an online clustering algorithm designed for real-time phylogenetic analysis of genome streams, identifying species boundaries and dynamics with minimal integration effort.

Contribution

It introduces a novel, pluggable clustering method for streaming genomic data that operates alongside experimental protocols with minimal interaction.

Findings

Enables real-time phylogenetic analysis from genome streams

Identifies species boundaries and hybridism dynamics

Operates with minimal integration effort

Abstract

To tackle the challenge of producing tractable phylogenetic trees in contexts where complete information is available, we introduce APOGeT: an online, pluggable, clustering algorithm for a stream of genomes. It is designed to run alongside a given experimental protocol with minimal interactions and integration effort. From the genomic flow, it extracts and displays species' boundaries and dynamics. Starting with a light introduction to the core idea of this classification we discuss the requirements on the genomes and the underlying processes of building species' identities and managing hybridism. Though stemming from an ALife experimental setting, APOGeT ought not be limited to this field but could be used by (and benefit from) a broader audience.