@inbook{d435ff333e1f4067a9367edb208156b0,
title = "Studying evolutionary dynamics of gene families encoding SUMO-activating enzymes with SeaView and ProtTest",
abstract = "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).",
keywords = "Evolution model, Maximum likelihood, Multiple sequence alignment, Neighbor joining, Phylogenetic analysis",
author = "Lorenzo Carretero-Paulet and Albert, \{Victor A.\}",
note = "Publisher Copyright: {\textcopyright} Springer Science+Business Media New York 2016.",
year = "2016",
doi = "10.1007/978-1-4939-3759-2\_22",
language = "English",
series = "Methods in Molecular Biology",
publisher = "Humana Press Inc.",
pages = "273--284",
booktitle = "Methods in Molecular Biology",
}