Veidenberg Andres, Löytynoja Ari
Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
Methods Mol Biol. 2021;2231:225-240. doi: 10.1007/978-1-0716-1036-7_14.
Wasabi is an open-source, web-based graphical environment for evolutionary sequence analysis and visualization, designed to work with multiple sequence alignments within their phylogenetic context. Its interactive user interface provides convenient access to external data sources and computational tools and is easily extendable with custom tools and pipelines using a plugin system. Wasabi stores intermediate editing and analysis steps as workflow histories and provides direct-access web links to datasets, allowing for reproducible, collaborative research, and easy dissemination of the results. In addition to shared analyses and installation-free usage, the web-based design allows Wasabi to be run as a cross-platform, stand-alone application and makes its integration to other web services straightforward.This chapter gives a detailed description and guidelines for the use of Wasabi's analysis environment. Example use cases will give step-by-step instructions for practical application of the public Wasabi, from quick data visualization to branched analysis pipelines and publishing of results. We end with a brief discussion of advanced usage of Wasabi, including command-line communication, interface extension, offline usage, and integration to local and public web services. The public Wasabi application, its source code, documentation, and other materials are available at http://wasabiapp.org.
山葵（Wasabi）是一个基于网络的开源图形化环境，用于进化序列分析和可视化，旨在与系统发育背景下的多序列比对协同工作。其交互式用户界面便于访问外部数据源和计算工具，并可使用插件系统通过自定义工具和管道轻松扩展。山葵将中间编辑和分析步骤存储为工作流历史记录，并提供数据集的直接访问网络链接，支持可重复的协作研究以及结果的轻松传播。除了共享分析和免安装使用外，基于网络的设计使山葵能够作为跨平台独立应用程序运行，并使其与其他网络服务的集成变得简单直接。本章详细介绍了山葵分析环境的使用方法和指南。示例用例将为公共山葵的实际应用提供逐步指导，从快速数据可视化到分支分析管道以及结果发布。最后，我们简要讨论了山葵的高级用法，包括命令行通信、界面扩展、离线使用以及与本地和公共网络服务的集成。公共山葵应用程序及其源代码、文档和其他材料可在http://wasabiapp.org获取。
