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EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences

Abstract (Expand)

Next generation sequencing (NGS) technologies have led to a ubiquity of molecular sequence data. This data avalanche is particularly challenging in metagenetics, which focuses on taxonomic identification … of sequences obtained from diverse microbial environments. Phylogenetic placement methods determine how these sequences fit into an evolutionary context. Previous implementations of phylogenetic placement algorithms, such as the evolutionary placement algorithm (EPA) included in RAxML, or PPLACER, are being increasingly used for this purpose. However, due to the steady progress in NGS technologies, the current implementations face substantial scalability limitations. Herein, we present EPA-NG, a complete reimplementation of the EPA that is substantially faster, offers a distributed memory parallelization, and integrates concepts from both, RAxML-EPA and PPLACER. EPA-NG can be executed on standard shared memory, as well as on distributed memory systems (e.g., computing clusters). To demonstrate the scalability of EPA-NG, we placed 1 billion metagenetic reads from the Tara Oceans Project onto a reference tree with 3748 taxa in just under 7 h, using 2048 cores. Our performance assessment shows that EPA-NG outperforms RAxML-EPA and PPLACER by up to a factor of 30 in sequential execution mode, while attaining comparable parallel efficiency on shared memory systems. We further show that the distributed memory parallelization of EPA-NG scales well up to 2048 cores. EPA-NG is available under the AGPLv3 license: https://github.com/Pbdas/epa-ng.

Authors: Pierre Barbera, Alexey M Kozlov, Lucas Czech, Benoit Morel, Diego Darriba, Tomáš Flouri, Alexandros Stamatakis

Date Published: 2018

Publication Type: Journal

Phylogenomics and the evolution of hemipteroid insects

Abstract

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Authors: Kevin P Johnson, Christopher H Dietrich, Frank Friedrich, Rolf G Beutel, Benjamin Wipfler, Ralph S Peters, Julie M Allen, Malte Petersen, Alexander Donath, Kimberly KO Walden, others

Date Published: 2018

Publication Type: Journal

A roadmap for global synthesis of the plant tree of life

Abstract

Not specified

Authors: Wolf L Eiserhardt, Alexandre Antonelli, Dominic J Bennett, Laura R Botigué, J Gordon Burleigh, Steven Dodsworth, Brian J Enquist, Félix Forest, Jan T Kim, Alexey M Kozlov, others

Date Published: 2018

Publication Type: Journal

Clarifying the Relationships between Microsporidia and Cryptomycota

Abstract

Not specified

Authors: David Bass, Lucas Czech, Bryony AP Williams, Cédric Berney, Micah Dunthorn, Frederic Mahé, Guifré Torruella, Grant D Stentiford, Tom A Williams

Date Published: 2018

Publication Type: Journal

New data, same story: phylogenomics does not support Syrphoidea (Diptera: Syrphidae, Pipunculidae)

Abstract

Not specified

Authors: Thomas Pauli, Trevor O Burt, Karen Meusemann, Keith Bayless, Alexander Donath, Lars Podsiadlowski, Christoph Mayer, Alexey Kozlov, Alexandros Vasilikopoulos, Shanlin Liu, others

Date Published: 2018

Publication Type: Journal

Phylogenomic analysis of Apoidea sheds new light on the sister group of bees

Abstract

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Authors: Manuela Sann, Oliver Niehuis, Ralph S Peters, Christoph Mayer, Alexey Kozlov, Lars Podsiadlowski, Sarah Bank, Karen Meusemann, Bernhard Misof, Christoph Bleidorn, others

Date Published: 2018

Publication Type: Journal

Transcriptome sequence-based phylogeny of chalcidoid wasps (Hymenoptera: Chalcidoidea) reveals a history of rapid radiations, convergence, and evolutionary success

Abstract

Not specified

Authors: Ralph S Peters, Oliver Niehuis, Simon Gunkel, Marcel Bläser, Christoph Mayer, Lars Podsiadlowski, Alexey Kozlov, Alexander Donath, Simon van Noort, Shanlin Liu, others

Date Published: 2018

Publication Type: Journal

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