Centre for Computational Evolution, University of Auckland, Auckland, New Zealand.
School of Biological Sciences, University of Auckland, Auckland, New Zealand.
PLoS Comput Biol. 2023 Jul 18;19(7):e1011226. doi: 10.1371/journal.pcbi.1011226. eCollection 2023 Jul.
Phylogenetic models have become increasingly complex, and phylogenetic data sets have expanded in both size and richness. However, current inference tools lack a model specification language that can concisely describe a complete phylogenetic analysis while remaining independent of implementation details. We introduce a new lightweight and concise model specification language, 'LPhy', which is designed to be both human and machine-readable. A graphical user interface accompanies 'LPhy', allowing users to build models, simulate data, and create natural language narratives describing the models. These narratives can serve as the foundation for manuscript method sections. Additionally, we present a command-line interface for converting LPhy-specified models into analysis specification files (in XML format) compatible with the BEAST2 software platform. Collectively, these tools aim to enhance the clarity of descriptions and reporting of probabilistic models in phylogenetic studies, ultimately promoting reproducibility of results.
系统发育模型变得越来越复杂，系统发育数据集在大小和丰富度上都有所扩展。然而，目前的推断工具缺乏一种模型指定语言，可以简洁地描述完整的系统发育分析，同时独立于实现细节。我们引入了一种新的轻量级和简洁的模型指定语言“LPhy”，它旨在同时具有人类可读性和机器可读性。“LPhy”有一个图形用户界面，允许用户构建模型、模拟数据，并创建描述模型的自然语言叙述。这些叙述可以作为手稿方法部分的基础。此外，我们还提供了一个命令行界面，用于将 LPhy 指定的模型转换为可与 BEAST2 软件平台兼容的分析指定文件（XML 格式）。这些工具旨在提高系统发育研究中概率模型描述和报告的清晰度，最终促进结果的可重复性。
