MrsRF: an efficient MapReduce algorithm for analyzing large collections of evolutionary trees.

BMC Bioinformatics
Suzanne J Matthews, Tiffani L Williams

Abstract

MapReduce is a parallel framework that has been used effectively to design large-scale parallel applications for large computing clusters. In this paper, we evaluate the viability of the MapReduce framework for designing phylogenetic applications. The problem of interest is generating the all-to-all Robinson-Foulds distance matrix, which has many applications for visualizing and clustering large collections of evolutionary trees. We introduce MrsRF (MapReduce Speeds up RF), a multi-core algorithm to generate a t x t Robinson-Foulds distance matrix between t trees using the MapReduce paradigm. We studied the performance of our MrsRF algorithm on two large biological trees sets consisting of 20,000 trees of 150 taxa each and 33,306 trees of 567 taxa each. Our experiments show that MrsRF is a scalable approach reaching a speedup of over 18 on 32 total cores. Our results also show that achieving top speedup on a multi-core cluster requires different cluster configurations. Finally, we show how to use an RF matrix to summarize collections of phylogenetic trees visually. Our results show that MapReduce is a promising paradigm for developing multi-core phylogenetic applications. The results also demonstrate that different multi-core c...Continue Reading

References

Aug 10, 2002·Bioinformatics·Cara StockhamTandy Warnow
Jul 14, 2005·Systematic Biology·David M HillisKatherine St John
Dec 13, 2005·Systematic Biology·Louise A Lewis, Paul O Lewis
Apr 10, 2009·Bioinformatics·Michael C Schatz
May 14, 2009·BMC Bioinformatics·Seung-Jin SulTiffani L Williams
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin

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Citations

Jul 14, 2010·Nature Biotechnology·Michael C SchatzSteven L Salzberg
Jan 9, 2013·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Hong Huang, Yongji Li
Aug 20, 2011·Source Code for Biology and Medicine·Marc E ColosimoLynette Hirschman
Feb 16, 2016·Genomics, Proteomics & Bioinformatics·Pingjian Yu, Wei Lin
Sep 12, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Suzanne J Matthews
Jul 23, 2013·Journal of Biomedical Informatics·Aisling O'DriscollRoy D Sleator
Aug 12, 2021·Bioinformatics and Biology Insights·Saraswati KoppadAnimesh Acharjee

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Software Mentioned

MapReduce
MrBayes
CloudBurst
Linux
Google indexing
Hadoop
Phoenix
HashRF
OpenMPI
MapReduce Speeds up RF

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