Parallel Inference of Phylogenetic Stands with Gentrius DOI
Anastasis Togkousidis, Olga Chernomor, Alexandros Stamatakis

et al.

2022 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), Journal Year: 2023, Volume and Issue: unknown, P. 139 - 148

Published: May 1, 2023

Multi-locus datasets are frequently used to infer phylogenies instead of using single locus. Missing data constitute a common challenge in such as they can lead stands, that is, sets trees compatible with the incomplete per-locus trees. Under many criteria from one stand have identical score. Hence, identifying stands and determining their sizes is crucial importance for robust phylogenetic analysis. Recently, Chernomor et al. published Gentrius, branch-and-bound algorithm enumerates all given set unrooted locus Despite its efficiency, pattern proportion missing multi-locus still induce extremely long execution times.Here, we introduce parallel version Gentrius algorithm. Our parallelization deploys thread-pooling mechanism maintains threads finish early busy-wait mode, contribute solving long-running tasks. Thereby, substantially reduce load imbalance attain high efficiency. performance assessment up 16 cores yields linear speedups on both, simulated, empirical data. The available open source code under GNU GPL at https://github.com/togkousa/iqtree2/tree/terragen. All our analyses, download https://cme.h-its.oryexelixis/material/gentrius-parallel.tar.gz.

Language: Английский

Parallel Inference of Phylogenetic Stands with Gentrius DOI
Anastasis Togkousidis, Olga Chernomor, Alexandros Stamatakis

et al.

2022 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), Journal Year: 2023, Volume and Issue: unknown, P. 139 - 148

Published: May 1, 2023

Multi-locus datasets are frequently used to infer phylogenies instead of using single locus. Missing data constitute a common challenge in such as they can lead stands, that is, sets trees compatible with the incomplete per-locus trees. Under many criteria from one stand have identical score. Hence, identifying stands and determining their sizes is crucial importance for robust phylogenetic analysis. Recently, Chernomor et al. published Gentrius, branch-and-bound algorithm enumerates all given set unrooted locus Despite its efficiency, pattern proportion missing multi-locus still induce extremely long execution times.Here, we introduce parallel version Gentrius algorithm. Our parallelization deploys thread-pooling mechanism maintains threads finish early busy-wait mode, contribute solving long-running tasks. Thereby, substantially reduce load imbalance attain high efficiency. performance assessment up 16 cores yields linear speedups on both, simulated, empirical data. The available open source code under GNU GPL at https://github.com/togkousa/iqtree2/tree/terragen. All our analyses, download https://cme.h-its.oryexelixis/material/gentrius-parallel.tar.gz.

Language: Английский

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