Computational Grand Challenges in Assembling the Tree of Life: Problems and Solutions

David A. Bader, Usman Roshan, Alexandros Stamatakis

Research output: Chapter in Book/Report/Conference proceedingChapter

26 Scopus citations

Abstract

The computation of ever larger as well as more accurate phylogenetic (evolutionary) trees with the ultimate goal to compute the tree of life represents one of the grand challenges in High Performance Computing (HPC) Bioinformatics. Unfortunately, the size of trees which can be computed in reasonable time based on elaborate evolutionary models is limited by the severe computational cost inherent to these methods. There exist two orthogonal research directions to overcome this challenging computational burden: First, the development of novel, faster, and more accurate heuristic algorithms and second, the application of high performance computing techniques. The goal of this chapter is to provide a comprehensive introduction to the field of computational evolutionary biology to an audience with computing background, interested in participating in research and/or commercial applications of this field. Moreover, we will cover leading-edge technical and algorithmic developments in the field and discuss open problems and potential solutions.

Original languageEnglish (US)
Title of host publicationComputational Biology and Bioinformatics
EditorsChau-Wen Tseng
Pages127-176
Number of pages50
DOIs
StatePublished - 2006

Publication series

NameAdvances in Computers
Volume68
ISSN (Print)0065-2458

All Science Journal Classification (ASJC) codes

  • Computer Science(all)

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