Data from: Phylotocol: promoting transparency and overcoming bias in phylogenetics

The integrity of science requires that the process be based on sound
experimental design and objective methodology. Strategies that increase
reproducibility and transparency in science protect this integrity by
reducing conscious and unconscious biases. Given the large number of
analysis options and the constant development of new methodologies in
phylogenetics, this field is one that would particularly benefit from more
transparent research design. Here, we introduce phylotocol
(fī·lō·´tə·kôl), an a priori protocol-driven approach in which all
analyses are planned and documented at the start of a project. The
phylotocol template is simple and the implementation options are flexible
to reduce administrative burdens and allow researchers to adapt it to
their needs without restricting scientific creativity. While the primary
goal of phylotocol is to increase transparency and accountability, it has
a number of auxiliary benefits including improving study design and
reproducibility, enhancing collaboration and education, and increasing the
likelihood of project completion. Our goal with this Point of View article
is to encourage a dialogue about transparency in phylogenetics and the
best strategies to bring transparent research practices to our field.