Pourmohsenin Bita, Wiese Arthur, Ziemert Nadine
Translational Genome Mining for Natural Products, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Tübingen, Baden-Württemberg 72076, Germany.
German Center for Infection Research (DZIF), Partner Site Tübingen, 72076, Tübingen, Germany.
Nucleic Acids Res. 2025 Jul 7;53(W1):W45-W50. doi: 10.1093/nar/gkaf397.
Accurate and accessible phylogenetic analysis is essential for understanding microbial taxonomy and evolution, which are integral to microbiology, ecology, and drug discovery, yet it remains a challenging task. AutoMLST2 (https://automlst2.ziemertlab.com) is a web server designed to facilitate automated phylogenetic reconstruction and microbial taxonomy analysis for bacterial and archaeal genomes. It builds on the foundation of AutoMLST, which remains widely used due to its user-friendly interface compared to similar tools. Given its continued popularity and utility, we have enhanced AutoMLST to leverage newer reference databases and computational tools. AutoMLST2 integrates the Genome Taxonomy Database, extends support to archaeal genomes, and improves analytical flexibility. Key improvements include more customizable processing modes, containerization to prevent queue accumulations, and parallel computing for large-scale studies. By incorporating up-to-date databases and workflows, AutoMLST2 continues to provide an accessible and efficient platform for researchers in microbiology, evolutionary ecology, and natural product discovery.
准确且易于使用的系统发育分析对于理解微生物分类学和进化至关重要，而微生物分类学和进化是微生物学、生态学及药物发现不可或缺的一部分，但这仍然是一项具有挑战性的任务。AutoMLST2（https://automlst2.ziemertlab.com）是一个网络服务器，旨在促进对细菌和古菌基因组进行自动系统发育重建和微生物分类学分析。它基于AutoMLST构建，与类似工具相比，AutoMLST因其用户友好的界面而仍被广泛使用。鉴于其持续的受欢迎程度和实用性，我们对AutoMLST进行了改进，以利用更新的参考数据库和计算工具。AutoMLST2整合了基因组分类数据库，扩展了对古菌基因组的支持，并提高了分析灵活性。主要改进包括更可定制的处理模式、采用容器化以防止队列堆积，以及针对大规模研究的并行计算。通过纳入最新的数据库和工作流程，AutoMLST2继续为微生物学、进化生态学和天然产物发现领域的研究人员提供一个易于使用且高效的平台。
