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.Appendix_1Blank phylotocol template in Word formatAppendix_2Blank phylotocol template in markdown formatAppendix_3Example phylotocol in markdown format. This document describes the analysis plan for an empirical phylogenomic study. Title: Planned analysis for testing holothurian phylogeny and developing target enrichment baitsAppendix_4Example phylotocol in PDF format. This document describes the analysis plan for a phylogenetic simulation study. Title: An extension of testing 6-state recoding strategies to address substitution bias and compositional heterogeneityAppendix_5Example phylotocol in PDF format. This document describes the analysis plan for an empirical phylogenomic study. Title: Planned analyses for testing existence of sponge parahoxFunding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: 154259