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).
authors.affiliation: Department of Plant Systems Biology, VIB, Ghent University, Technologiepark 927, 9052, Ghent, Belgium. locar@psb.ugent.be.
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Carretero-Paulet
authors.affiliation: Department of Biological Sciences, SUNY-University at Buffalo, 109 Cooke Hall, Buffalo, NY, 14260-4610, USA.
authors.forename: Victor A
authors.initials: VA
authors.lastname: Albert
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D019143:Evolution, Molecular; D008957:Models, Genetic; D005810:Multigene Family / Q000235:genetics*; D010802:Phylogeny; D011506:Proteins / Q000737:chemistry; D016415:Sequence Alignment / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins
keywords: Evolution model; Maximum likelihood; Multiple sequence alignment; Neighbor joining; Phylogenetic analysis