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https://doi.org/10.1...arrow_drop_down
https://doi.org/10.1007/115576...
Part of book or chapter of book . 2005 . Peer-reviewed
Data sources: Crossref
DBLP
Conference object . 2024
Data sources: DBLP
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Parallel Divide-and-Conquer Phylogeny Reconstruction by Maximum Likelihood

Authors: Z. Du; Alexandros Stamatakis; F. Lin; Usman Roshan; Luay Nakhleh;

Parallel Divide-and-Conquer Phylogeny Reconstruction by Maximum Likelihood

Abstract

Phylogenetic trees are important in biology since their applications range from determining protein function to understanding the evolution of species. Maximum Likelihood (ML) is a popular optimization criterion in phylogenetics. However, inference of phylogenies with ML is NP-hard. Recursive-Iterative-DCM3 (Rec-I-DCM3) is a divide-and-conquer framework that divides a dataset into smaller subsets (subproblems), applies an external base method to infer subtrees, merges the subtrees into a comprehensive tree, and then refines the global tree with an external global method. In this study we present a novel parallel implementation of Rec-I-DCM3 for inference of large trees with ML. Parallel-Rec-I-DCM3 uses RAxML as external base and global search method. We evaluate program performance on 6 large real-data alignments containing 500 up to 7.769 sequences. Our experiments show that P-Rec-I-DCM3 reduces inference times and improves final tree quality over sequential Rec-I-DCM3 and stand-alone RAxML.

Country
Germany
Keywords

ddc:004, DATA processing & computer science, info:eu-repo/classification/ddc/004, 004

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Found an issue? Give us feedback
selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
7
Average
Average
Top 10%
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