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104 Publications visible to you, out of a total of 104
Metagenomic Analysis Using Phylogenetic Placement—A Review of the First Decade

Abstract

Not specified

Authors: Lucas Czech, Alexandros Stamatakis, Micah Dunthorn, Pierre Barbera

Date Published: 26th May 2022

Publication Type: Journal

Lagrange-NG: The next generation of Lagrange

Abstract

Not specified

Authors: Ben Bettisworth, Stephen A. Smith, Alexandros Stamatakis

Date Published: 20th Apr 2022

Publication Type: Journal

Core-Count Independent Reproducible Reduce

Abstract (Expand)

ecause of rounding errors, parallel floating-point summation can produce different results on different core-counts. For some algorithms like hill climbing, RAxML-NG [7] or greedy algorithms, this … implies that results may be irreproducible with different core-counts. We present the Binary Tree Reduction algorithm, which follows a distributed binary tree scheme that keeps the calculation order fixed and independent of the core-count 푝. A naive implementation requires up to (푝 − 1) ∗ (log2 ( 푁 −1 푝 ) + 1) messages to sum 푁 floating-point numbers. To reduce the message count, we introduce a message buffer and optimize data distribution across the cores, the latter results in a runtime decrease of 18 %. We find that for 푝 = 256, Binary Tree Reduction has a slowdown of less than 2 compared to a naive, irreproducible solution. It is able to compute the sum of 푁 ≈ 21 ∗ 106 summands on 푝 = 256 cores in about 248 μs.

Authors: Christoph Stelz, Lukas Hübner, Alexandros Stamatakis

Date Published: 1st Apr 2022

Publication Type: Bachelor's Thesis

SPART: A versatile and standardized data exchange format for species partition information

Abstract

Not specified

Authors: Aurélien Miralles, Jacques Ducasse, Sophie Brouillet, Tomas Flouri, Tomochika Fujisawa, Paschalia Kapli, L. Lacey Knowles, Sangeeta Kumari, Alexandros Stamatakis, Jeet Sukumaran, Sarah Lutteropp, Miguel Vences, Nicolas Puillandre

Date Published: 2022

Publication Type: Journal

RAxML Grove: An empirical Phylogenetic Tree Database

Abstract

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Authors: Dimitri Höhler, Wayne Pfeiffer, Vassilios Ioannidis, Heinz Stockinger, Alexandros Stamatakis

Date Published: 6th Oct 2021

Publication Type: Journal

NetRAX: Accurate and Fast Maximum Likelihood Phylogenetic Network Inference ⋆

Abstract

Not specified

Authors: Sarah Lutteropp, Céline Scornavacca, Alexey M. Kozlov, Benoit Morel, Alexandros Stamatakis

Date Published: 31st Aug 2021

Publication Type: Journal

Swarm v3: towards tera-scale amplicon clustering

Abstract

Not specified

Authors: Frédéric Mahé, Lucas Czech, Alexandros Stamatakis, Christopher Quince, Colomban de Vargas, Micah Dunthorn, Torbjørn Rognes

Date Published: 9th Jul 2021

Publication Type: Journal

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