title: A practical guide to phylogenetics for nonexperts.
abstract: Many researchers, across incredibly diverse foci, are applying phylogenetics to their research question(s). However, many researchers are new to this topic and so it presents inherent problems. Here we compile a practical introduction to phylogenetics for nonexperts. We outline in a step-by-step manner, a pipeline for generating reliable phylogenies from gene sequence datasets. We begin with a user-guide for similarity search tools via online interfaces as well as local executables. Next, we explore programs for generating multiple sequence alignments followed by protocols for using software to determine best-fit models of evolution. We then outline protocols for reconstructing phylogenetic relationships via maximum likelihood and Bayesian criteria and finally describe tools for visualizing phylogenetic trees. While this is not by any means an exhaustive description of phylogenetic approaches, it does provide the reader with practical starting information on key software applications commonly utilized by phylogeneticists. The vision for this article would be that it could serve as a practical training tool for researchers embarking on phylogenetic studies and also serve as an educational resource that could be incorporated into a classroom or teaching-lab.
authors.affiliation: Department of Biological Sciences and Institute for Neuroscience, The George Washington University; damienoh@gwu.edu.
authors.forename: Damien
authors.initials: D
authors.lastname: O'Halloran
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D001499:Bayes Theorem; D016013:Likelihood Functions; D010802:Phylogeny; D016415:Sequence Alignment / Q000379:methods*; D017421:Sequence Analysis / Q000379:methods*; D012984:Software