Genetic Analysis

Gavin J.D. Smith, Justin Bahl, Dhanasekaran Vijaykrishna

Research output: Chapter in Book/Report/Conference proceedingChapter (Book)Otherpeer-review


Genetic analysis of sequence data is central to determining the evolutionary history and molecular epidemiology of viruses, particularly those such as infl uenza A virus that have complex ecosystems involving multiple hosts. Here we provide an outline of routine phylogenetic analyses of infl uenza A viruses including multiple sequence alignment, selecting the best-fi t evolutionary model and phylogenetic tree reconstruction using Neighbor joining, Maximum likelihood, and Bayesian inference.
Original languageEnglish
Title of host publicationInfluenza virus
Subtitle of host publicationMethods and protocols
EditorsYoshihiro Kawaoka, Gabriele Neumann
Place of PublicationUSA
Number of pages21
ISBN (Electronic)978-1-61779-621-0
ISBN (Print)978-1-61779-620-3
Publication statusPublished - 2012
Externally publishedYes

Publication series

NameMethods in Molecular Biology
PublisherSpringer Science+Business Media, LLC 2012
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029


  • sequence alignment
  • phylogeny
  • evolution
  • natural selection
  • neighbour joining
  • maximum likelihood
  • bayesian inference

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