LinguaPhylo: a probabilistic model specification language for reproducible phylogenetic analyses

Phylogenetic models have become increasingly complex and phylogenetic data sets larger and richer. Yet inference tools lack a model specification language that succinctly describes a full phylogenetic analysis independently of implementation details. We present a new lightweight and concise model specification language, called ‘LPhy’, that is both human and machine readable. ‘LPhy’ is accompanied by a graphical user interface for building models and simulating data using this new language, as well as for creating natural language narratives describing such models. These narratives can form the basis of manuscript method sections. We also introduce a command-line interface for converting LPhy-specified models into analysis specification files (in XML format) to be used alongside the BEAST2 software platform. Together, these tools will clarify the description and reporting of probabilistic models in phylogenetic studies, and improve result reproducibility. Author summary We describe a succinct domain-specific language to accurately specify the details of a phylogenetic model for the purposes of reproducibility or reuse. In addition, we have developed a graphical software package that can be used to construct and simulate data from models described in this new language, as well as create natural language narratives that can form the basis of a description of the model for the method section of a manuscript. Finally, we report on a command-line program that can be used to generate input files for the BEAST2 software package based on a model specified in this new language. These tools together should aid in the goal of reproducibility and reuse of probabilistic phylogenetic models. ### Competing Interest Statement The authors have declared no competing interest.