title: Wasabi: An Integrated Platform for Evolutionary Sequence Analysis and Data Visualization.
abstract: 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.
authors.affiliation: Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
authors.forename: Andres
authors.initials: A
authors.lastname: Veidenberg
authors.affiliation: Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
authors.forename: Alan
authors.initials: A
authors.lastname: Medlar
authors.affiliation: Institute of Biotechnology, University of Helsinki, Helsinki, Finland ari.loytynoja@helsinki.fi.
authors.forename: Ari
authors.initials: A
authors.lastname: Löytynoja
mesh_terms: D000465:Algorithms; D019143:Evolution, Molecular; D016678:Genome; D020407:Internet; D010802:Phylogeny; D016415:Sequence Alignment; D017421:Sequence Analysis / Q000379:methods*; D017422:Sequence Analysis, DNA; D012984:Software; D064878:Web Browser
keywords: data visualization; evolutionary sequence analysis; reproducible research