title: An Integrated Perspective on Phylogenetic Workflows.
abstract: Molecular phylogenetics is the study of evolutionary relationships between biological sequences, often to infer the evolutionary relationships of organisms. These studies require many analysis components, including sequence assembly, identification of homologous sequences, gene tree inference, and species tree inference. At present, each component is usually treated as a single step in a linear analysis, where the output of each component is passed as input to the next as a point estimate. Here we outline a generative model that helps clarify assumptions that are implicit to phylogenetic workflows, focusing on the assumption of low relative entropy. This perspective unifies currently disparate advances, and will help investigators evaluate which steps would benefit the most from additional computation and future methods development.
authors.affiliation: Department of Applied Math, Brown University, 182 George St, Providence, RI 02906, USA; Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman St, Providence, RI 02912, USA.
authors.forename: August
authors.initials: A
authors.lastname: Guang
authors.affiliation: Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman St, Providence, RI 02912, USA.
authors.forename: Felipe
authors.initials: F
authors.lastname: Zapata
authors.affiliation: Computing and Information Services, Brown University, 3 Davol Sq., Providence, RI 02903, USA.
authors.forename: Mark
authors.initials: M
authors.lastname: Howison
authors.affiliation: Department of Applied Math, Brown University, 182 George St, Providence, RI 02906, USA.
authors.forename: Charles E
authors.initials: CE
authors.lastname: Lawrence
authors.affiliation: Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman St, Providence, RI 02912, USA. Electronic address: casey_dunn@brown.edu.
authors.forename: Casey W
authors.initials: CW
authors.lastname: Dunn
mesh_terms: D000818:Animals; D019295:Computational Biology; D019143:Evolution, Molecular; D051456:Gene Flow; D010802:Phylogeny; D012984:Software; D013045:Species Specificity