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Data Distribution for Phylogenetic Inference with Site Repeats via Judicious Hypergraph Partitioning

Ivo Baar, Lukas Hübner, Peter Oettig, Adrian Zapletal, Sebastian Schlag, Alexandros Stamatakis, Benoit Morel
doi: https://doi.org/10.1101/579318
Ivo Baar
Institute for Theoretical Informatics Karlsruhe Institute of Technology Karlsruhe, Germany
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Lukas Hübner
Institute for Theoretical Informatics Karlsruhe Institute of Technology Karlsruhe, Germany
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Peter Oettig
Institute for Theoretical Informatics Karlsruhe Institute of Technology Karlsruhe, Germany
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Adrian Zapletal
Institute for Theoretical Informatics Karlsruhe Institute of Technology Karlsruhe, Germany
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Sebastian Schlag
Institute for Theoretical Informatics Karlsruhe Institute of Technology Karlsruhe, Germany
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Alexandros Stamatakis
Institute for Theoretical Informatics Karlsruhe Institute of Technology Karlsruhe, Germany
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Benoit Morel
Computational Molecular Evolution group Heidelberg Institute for Theoretical Studies Heidelberg, Germany
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Abstract

The so-called site repeats (SR) technique can be used to accelerate the widely-used phylogenetic likelihood function (PLF) by identifying identical patterns among multiple sequence alignment (MSA) sites, thereby omitting redundant calculations and saving memory. However, this complicates the optimal data distribution of MSA sites in parallel likelihood calculations, as the cost of computing the likelihood for individual sites strongly depends on the sites-to-cores assignment. We show that finding a ‘good’ sites-to-cores assignment can be modeled as a hypergraph partitioning problem, more specifically, a specific instance of the so-called judicious hypergraph partitioning problem. We initially develop, parallelize, and make available HyperPhylo, an efficient open-source implementation for this flavor of judicious partitioning where all vertices have the same degree. Using empirical MSA data, we then show that sites-to-core assignments computed via HyperPhylo are substantially better than those obtained via a previous na ï ve approach for phylogenetic data distribution under SRs.

Footnotes

  • alexandros.stamatakis{at}kit.edu, sebastian.schlag{at}kit.edu

  • benoit.morel{at}h-its.org

  • Part of this work was supported by the Klaus-Tschira foundation and DFG grant STA 860/6-1.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted March 18, 2019.
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Data Distribution for Phylogenetic Inference with Site Repeats via Judicious Hypergraph Partitioning
Ivo Baar, Lukas Hübner, Peter Oettig, Adrian Zapletal, Sebastian Schlag, Alexandros Stamatakis, Benoit Morel
bioRxiv 579318; doi: https://doi.org/10.1101/579318
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Data Distribution for Phylogenetic Inference with Site Repeats via Judicious Hypergraph Partitioning
Ivo Baar, Lukas Hübner, Peter Oettig, Adrian Zapletal, Sebastian Schlag, Alexandros Stamatakis, Benoit Morel
bioRxiv 579318; doi: https://doi.org/10.1101/579318

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