Fine Grain Parallel Construction of Neighbour-joining Phylogenetic Trees with Reduced Redundancy Using Multithreading

Sahoo, Biswajit; Behura, Ashutosh; Padhy, Sudarsan

doi:10.5121/ijdps.2010.1211

Cited by 1 publication

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References 11 publications

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“…For example, Rucci et al (2013) presented a parallel algorithm for neighbor joining based on the multicore cluster, Sahoo et al (2010) proposed a parallel algorithm based on the Pthread library, and Al-Neama et al (2014) implemented a parallel algorithm on OpenMP. In addition, Du and Feng (2006) proposed the pNJTree parallel method for neighbor joining using a message passing interface (MPI) running on a workstation cluster, and Liu et al (2009) developed a parallel neighbor joining algorithm based on GPUs.…”

Section: Introductionmentioning

confidence: 99%

Methodology A fast neighbor joining method

2015

Genet. Mol. Res.

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ABSTRACT. With the rapid development of sequencing technologies, an increasing number of sequences are available for evolutionary tree reconstruction. Although neighbor joining is regarded as the most popular and fastest evolutionary tree reconstruction method [its time complexity is O(n 3 ), where n is the number of sequences], it is not sufficiently fast to infer evolutionary trees containing more than a few hundred sequences. To increase the speed of neighbor joining, we herein propose FastNJ, a fast implementation of neighbor joining, which was motivated by RNJ and FastJoin, two improved versions of conventional neighbor joining. The main difference between FastNJ and conventional neighbor joining is that, in the former, many pairs of nodes selected by the rule used in RNJ are joined in each iteration. In theory, the time complexity of FastNJ can reach O(n 2 ) in the best cases. Experimental results show that FastNJ yields a significant increase in speed compared to RNJ and conventional neighbor joining with a minimal loss of accuracy.

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Section: Introductionmentioning

confidence: 99%

Methodology A fast neighbor joining method

2015

Genet. Mol. Res.

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Fine Grain Parallel Construction of Neighbour-joining Phylogenetic Trees with Reduced Redundancy Using Multithreading

Abstract: In biological research, scientists often need to use the information of the species to infer INDEX TERMPair wise alignment, operational taxonomic unit, phylogenetic tree, multiple sequence alignment.

Cited by 1 publication

References 11 publications

Methodology A fast neighbor joining method

Methodology A fast neighbor joining method

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