Literature DB >> 28476995

Parallel implementation of D-Phylo algorithm for maximum likelihood clusters.

Shamita Malik1, Dolly Sharma2, Sunil Kumar Khatri3.   

Abstract

This study explains a newly developed parallel algorithm for phylogenetic analysis of DNA sequences. The newly designed D-Phylo is a more advanced algorithm for phylogenetic analysis using maximum likelihood approach. The D-Phylo while misusing the seeking capacity of k-means keeps away from its real constraint of getting stuck at privately conserved motifs. The authors have tested the behaviour of D-Phylo on Amazon Linux Amazon Machine Image(Hardware Virtual Machine)i2.4xlarge, six central processing unit, 122 GiB memory, 8 × 800 Solid-state drive Elastic Block Store volume, high network performance up to 15 processors for several real-life datasets. Distributing the clusters evenly on all the processors provides us the capacity to accomplish a near direct speed if there should arise an occurrence of huge number of processors.

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Year:  2017        PMID: 28476995      PMCID: PMC8676462          DOI: 10.1049/iet-nbt.2016.0005

Source DB:  PubMed          Journal:  IET Nanobiotechnol        ISSN: 1751-8741            Impact factor:   1.847


  23 in total

1.  TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing.

Authors:  Heiko A Schmidt; Korbinian Strimmer; Martin Vingron; Arndt von Haeseler
Journal:  Bioinformatics       Date:  2002-03       Impact factor: 6.937

2.  Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses.

Authors:  Robert Lanfear; Brett Calcott; Simon Y W Ho; Stephane Guindon
Journal:  Mol Biol Evol       Date:  2012-01-20       Impact factor: 16.240

3.  New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

Authors:  Stéphane Guindon; Jean-François Dufayard; Vincent Lefort; Maria Anisimova; Wim Hordijk; Olivier Gascuel
Journal:  Syst Biol       Date:  2010-03-29       Impact factor: 15.683

4.  Phylogenetic mixture models for proteins.

Authors:  Si Quang Le; Nicolas Lartillot; Olivier Gascuel
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2008-12-27       Impact factor: 6.237

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Journal:  Trends Ecol Evol       Date:  1992-03       Impact factor: 17.712

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Authors:  N Saitou
Journal:  Methods Enzymol       Date:  1996       Impact factor: 1.600

7.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.

Authors:  J D Thompson; D G Higgins; T J Gibson
Journal:  Nucleic Acids Res       Date:  1994-11-11       Impact factor: 16.971

8.  Genome-scale phylogeny and the detection of systematic biases.

Authors:  Matthew J Phillips; Frédéric Delsuc; David Penny
Journal:  Mol Biol Evol       Date:  2004-04-14       Impact factor: 16.240

9.  A survey of combinatorial methods for phylogenetic networks.

Authors:  Daniel H Huson; Celine Scornavacca
Journal:  Genome Biol Evol       Date:  2010-11-15       Impact factor: 3.416

10.  qPMS9: an efficient algorithm for quorum Planted Motif Search.

Authors:  Marius Nicolae; Sanguthevar Rajasekaran
Journal:  Sci Rep       Date:  2015-01-15       Impact factor: 4.379

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