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Wasabi: An Integrated Platform for Evolutionary Sequence Analysis and Data Visualization
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DOI：10.1093/molbev/msv333.png)
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摘要
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Wasabi is an open source, web-based environment for evolutionary sequence analysis. Wasabi visualizes sequence data together with a phylogenetic tree within a modern, user-friendly interface: The interface hides extraneous options, supports context sensitive menus, drag-and-drop editing, and displays additional information, such as ancestral sequences, associated with specific tree nodes. The Wasabi environment supports reproducibility by automatically storing intermediate analysis steps and includes built-in functions to share data between users and publish analysis results. For computational analysis, Wasabi supports PRANK and PAGAN for phylogeny-aware alignment and alignment extension, and it can be easily extended with other tools. Along with drag-and-drop import of local files, Wasabi can access remote data through URL and import sequence data, GeneTrees and EPO alignments directly from Ensembl. To demonstrate a typical workflow using Wasabi, we reproduce key findings from recent comparative genomics studies, including a reanalysis of the EGLN1 gene from the tiger genome study: These case studies can be browsed within Wasabi at http://wasabiapp.org:8000?id=usecases. Wasabi runs inside a web browser and does not require any installation. One can start using it at http://wasabiapp.org. All source code is licensed under the AGPLv3.
Keyword:
evolutionary sequence analysis
reproducible research
data visualization
期刊
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5.3
论文数:
8.4K
被引数:
6.6W
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The Effect of Insertions, Deletions, and Alignment Errors on the Branch-Site Test of Positive Selection插入，缺失和比对错误对阳性选择的分支位点测试的影响
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