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. 2012:865:207-27.
doi: 10.1007/978-1-61779-621-0_13.

Genetic analysis

Gavin J D Smith  1 , Justin Bahl, Dhanasekaran Vijaykrishna
Affiliations

Genetic analysis

Gavin J D Smith et al. Methods Mol Biol. 2012.

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.

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Figures

Fig. 1.
Fig. 1.
The MAFFT terminal window.
Fig. 2.
Fig. 2.
The jModelTest console.
Fig. 3.
Fig. 3.
Settings for the likelihood calculations.
Fig. 4.
Fig. 4.
Settings for AIC model selection.
Fig. 5.
Fig. 5.
Results of the AIC model selection.
Fig. 6.
Fig. 6.
The PAUP* terminal window.
Fig. 7.
Fig. 7.
The MrBayes program window.
Fig. 8.
Fig. 8.
The Tracer program window.
Fig. 9.
Fig. 9.
State frequencies and summarizing trees in MrBayes.
Fig. 10.
Fig. 10.
Figtree: tree input.
Fig. 11.
Fig. 11.
Figtree.
See this image and copyright information in PMC

References

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Publication types

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