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.
Key wordsSequence alignment Phylogeny Evolution Natural selection Neighbor joining Maximum likelihood Bayesian inference
G.J.D.S. is supported by a career development award under National Institutes of Health, National Institute of Allergy and Infectious Disease contract HHSN266200700005C and G.J.D.S., J.B. and D.V. by the Duke–NUS Signature Research Program funded by the Agency for Science, Technology and Research, and the Ministry of Health, Singapore.
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