Molecular evolutionary analysis of gene families commonly involves a sequence of steps including multiple sequence alignment (MSA) and reconstructing phylogenetic trees, using any of the multiple algorithms available. SeaView is a multiplatform program that integrates different methods for performing the above tasks, and others, within a friendly and simple-to-use graphical user interface (Gouy et al. Mol Biol Evol 27(2):221–224, 2010). By using SeaView, we will investigate the evolutionary relationships among SAE1 genes in Brassicaceae species by means of two alternative methods of phylogenetic reconstruction: Maximum Likelihood (ML) and Neighbor-Joining (NJ). Prior to ML phylogenetic analysis (Guindon and Gascuel. Syst Biol 52(5):696–704, 2003), we will use ProtTest to select the best-fit evolutionary model of amino acid substitution for the MSA of SAE1 proteins (Abascal et al. Bioinformatics 21(9):2104–2105, 2005).
CITATION STYLE
Carretero-Paulet, L., & Albert, V. A. (2016). Studying evolutionary dynamics of gene families encoding SUMO-activating enzymes with SeaView and ProtTest. In Methods in Molecular Biology (Vol. 1450, pp. 273–284). Humana Press Inc. https://doi.org/10.1007/978-1-4939-3759-2_22
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