A parallel approach to Multiple sequences Alignment and phylogenetic tree node labelling

Wang Jingjing, Michelle Zhu

Research output: Contribution to journalArticleResearchpeer-review

Abstract

An evolutionary tree represents the relationship among a group of species or sequences. The quality of tree topology relies heavily on an efficient Multiple Sequence Alignment (MSA). Efficient and parallel algorithms are designed to utilise the computing power and memory in a supercomputer. A divide and conquer based parallel algorithm is implemented to perform optimal three sequence alignment with much reduced memory cost. All internal nodes generated from a parallel Maximum Likelihood tree software are labelled using our level order based parallel approach. Such node labelling process is also parallelised to lead to a two-level nested parallel computing strategy.

Original languageEnglish
Pages (from-to)226-236
Number of pages11
JournalInternational Journal of Computational Biology and Drug Design
Volume3
Issue number3
DOIs
StatePublished - 1 Dec 2010

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Sequence Alignment
Parallel algorithms
Labeling
Data storage equipment
Supercomputers
Parallel processing systems
Maximum likelihood
Software
Topology
Costs and Cost Analysis
Costs
Power (Psychology)

Keywords

  • MSA
  • Maximum Likelihood
  • Multiple Sequence Alignment
  • Parallel computing
  • Phylogenetic tree

Cite this

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A parallel approach to Multiple sequences Alignment and phylogenetic tree node labelling. / Jingjing, Wang; Zhu, Michelle.

In: International Journal of Computational Biology and Drug Design, Vol. 3, No. 3, 01.12.2010, p. 226-236.

Research output: Contribution to journalArticleResearchpeer-review

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