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Evolutionary Sequence Analysis and Visualization with Wasabi

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Multiple Sequence Alignment

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2231))

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Abstract

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

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Author information

Authors and Affiliations

  1. Institute of Biotechnology, University of Helsinki, Helsinki, Finland

    Andres Veidenberg & Ari Löytynoja

Authors
  1. Andres Veidenberg
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  2. Ari Löytynoja
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Corresponding author

Correspondence to Andres Veidenberg .

Editor information

Editors and Affiliations

  1. Research Institute for Microbial Disease, Osaka University, Osaka, Japan

    Kazutaka Katoh

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Veidenberg, A., Löytynoja, A. (2021). Evolutionary Sequence Analysis and Visualization with Wasabi. In: Katoh, K. (eds) Multiple Sequence Alignment. Methods in Molecular Biology, vol 2231. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1036-7_14

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  • DOI: https://doi.org/10.1007/978-1-0716-1036-7_14

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1035-0

  • Online ISBN: 978-1-0716-1036-7

  • eBook Packages: Springer Protocols

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