title: Genetic analysis.
abstract: Genetic analysis of sequence data is central to determining the evolutionary history and molecular epidemiology of viruses, particularly those such as influenza A virus that have complex ecosystems involving multiple hosts. Here we provide an outline of routine phylogenetic analyses of influenza A viruses including multiple sequence alignment, selecting the best-fit evolutionary model and phylogenetic tree reconstruction using Neighbor joining, Maximum likelihood, and Bayesian inference.
authors.affiliation: Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore, Singapore. gavin.smith@duke-nus.edu.sg
authors.forename: Gavin J D
authors.initials: GJ
authors.lastname: Smith
authors.forename: Justin
authors.initials: J
authors.lastname: Bahl
authors.forename: Dhanasekaran
authors.initials: D
authors.lastname: Vijaykrishna
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D001499:Bayes Theorem; D019143:Evolution, Molecular; D006801:Humans; D009980:Influenza A virus / Q000145:classification / Q000235:genetics; D007251:Influenza, Human / Q000453:epidemiology / Q000821:virology; D016013:Likelihood Functions; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics* / Q000302:isolation & purification; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D012367:RNA, Viral