An Integrated Perspective on Phylogenetic Workflows

Trends in Ecology & Evolution
August GuangCasey W Dunn

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.

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Citations

Jun 5, 2016·Genome Biology and Evolution·Benjamin J LiebeskindEdward M Marcotte
Jan 24, 2017·The Plant Journal : for Cell and Molecular Biology·Julian Tonti-FilippiniIan Small
Oct 4, 2016·The European Respiratory Journal·Gerard de VriesMichael Kimerling
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May 23, 2020·Current Zoology·Flavia Termignoni-GarciaScott V Edwards
Dec 2, 2020·Nature Communications·Xing-Xing ShenAntonis Rokas
Jan 13, 2021·PloS One·August GuangCasey W Dunn

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