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Studying Evolutionary Dynamics of Gene Families Encoding SUMO-Activating Enzymes with SeaView and ProtTest
- Source :
- Methods in Molecular Biology ISBN: 9781493937578
- Publication Year :
- 2016
- Publisher :
- Springer New York, 2016.
-
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).
- Subjects :
- 0106 biological sciences
0301 basic medicine
Genetics
Multiple sequence alignment
Phylogenetic tree
Computational biology
Biology
010603 evolutionary biology
01 natural sciences
03 medical and health sciences
030104 developmental biology
Encoding (memory)
Gene family
Evolutionary dynamics
Gene
Neighbor joining
Sequence (medicine)
Subjects
Details
- ISBN :
- 978-1-4939-3757-8
- ISBNs :
- 9781493937578
- Database :
- OpenAIRE
- Journal :
- Methods in Molecular Biology ISBN: 9781493937578
- Accession number :
- edsair.doi...........eca22a06dfa31bf529922b6ce438eb00