Koning Elizabeth, Subedi Arjun, Krishnakumar Raga
Biosecurity and Bioassurance Department, Sandia National Laboratories, Livermore, CA 94550, United States.
Department of Computer Science, University of Illinois, Urbana-Champaign, Urbana, IL 61801, United States.
Bioinform Adv. 2025 May 6;5(1):vbaf104. doi: 10.1093/bioadv/vbaf104. eCollection 2025.
Generating phylogenomic trees from the genomic data is essential in understanding biological systems. Each step of this complex process has received extensive attention and has been significantly streamlined over the years. Given the public availability of data, obtaining genomes for a wide selection of species is straightforward. However, analyzing that data to generate a phylogenomic tree is a multistep process with legitimate scientific and technical challenges, often requiring a significant input from a domain-area scientist.
We present Poplar, a new, streamlined computational pipeline, to address the computational logistical issues that arise when constructing the phylogenomic trees. It provides a framework that runs state-of-the-art software for essential steps in the phylogenomic pipeline, beginning from a genome with or without an annotation, and resulting in a species tree. Running Poplar requires no external databases. In the execution, it enables parallelism for execution for clusters and cloud computing. The trees generated by Poplar match closely with state-of-the-art published trees. The usage and performance of Poplar is far simpler and quicker than manually running a phylogenomic pipeline.
Freely available on GitHub at https://github.com/sandialabs/poplar. Implemented using Python and supported on Linux.
从基因组数据生成系统发育基因组树对于理解生物系统至关重要。这一复杂过程的每一步都受到了广泛关注，并且多年来已得到显著简化。鉴于数据的公开可用性，获取多种物种的基因组很简单。然而，分析这些数据以生成系统发育基因组树是一个多步骤过程，存在合理的科学和技术挑战，通常需要领域科学家大量投入。
我们展示了Poplar，这是一个新的、简化的计算流程，用于解决构建系统发育基因组树时出现的计算后勤问题。它提供了一个框架，运行用于系统发育基因组流程中关键步骤的最先进软件，从有或没有注释的基因组开始，最终生成物种树。运行Poplar不需要外部数据库。在执行过程中，它支持在集群和云计算上并行执行。Poplar生成的树与已发表的最先进的树非常匹配。Poplar的使用和性能比手动运行系统发育基因组流程要简单和快速得多。
可在GitHub上免费获取，网址为https://github.com/sandialabs/poplar。使用Python实现，支持在Linux上运行。
