EPA-ng

EPA-ng performs scalable phylogenetic placement of molecular sequences onto a reference phylogenetic tree to support taxonomic and evolutionary analysis of large next-generation sequencing datasets.

Key Features:

• Evolutionary Placement Algorithm Implementation: Reimplements the evolutionary placement algorithm (EPA) for phylogenetic placement of query sequences onto a fixed reference tree.
• High-Performance Phylogenetic Placement: Achieves substantial speed improvements compared with RAxML-EPA and pplacer for large-scale sequence datasets.
• Distributed Memory Parallelization: Supports distributed memory parallelization for execution on high-performance computing clusters.
• Shared and Distributed Memory Support: Executes on both shared-memory systems and distributed-memory computing environments.
• Integration of EPA Methodologies: Incorporates algorithmic concepts from RAxML-EPA and pplacer to improve scalability and performance.

Scientific Applications:

• Metagenomic Taxonomic Placement: Assigns environmental sequencing reads to positions on reference phylogenetic trees.
• Microbial Diversity Analysis: Investigates evolutionary relationships within complex microbial communities.
• Large-Scale Phylogenetic Studies: Processes large next-generation sequencing datasets for evolutionary and ecological analyses.

Methodology:

EPA-ng places query sequences onto a fixed reference phylogenetic tree using a reimplementation of the evolutionary placement algorithm with distributed and shared memory parallelization.