ArticleNucleic acids research2016
ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Theta-Defensins to Counter COVID-19 as Furin Inhibitors:Computational and mathematical methods in medicine · 2022Article
- Hotspots for mutations in the SARS-CoV-2 spike glycoprotein: a correspondence analysis.Scientific reports · 2021Article
- Plant expression of NifD protein variants resistant to mitochondrial degradation.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Tasks, Techniques, and Tools for Genomic Data Visualization.Computer graphics forum : journal of the European Association for Computer Graphics · 2019Article
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Authors and funding
8 authors.
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Abstract
Sequence Logos and its variants are the most commonly used method for visualization of multiple sequence alignments (MSAs) and sequence motifs. They provide consensus-based summaries of the sequences in the alignment. Consequently, individual sequences cannot be identified in the visualization and covariant sites are not easily discernible. We recently proposed Sequence Bundles, a motif visualization technique that maintains a one-to-one relationship between sequences and their graphical representation and visualizes covariant sites. We here present Alvis, an open-source platform for the joint explorative analysis of MSAs and phylogenetic trees, employing Sequence Bundles as its main visualization method. Alvis combines the power of the visualization method with an interactive toolkit allowing detection of covariant sites, annotation of trees with synapomorphies and homoplasies, and motif detection. It also offers numerical analysis functionality, such as dimension reduction and classification. Alvis is user-friendly, highly customizable and can export results in publication-quality figures. It is available as a full-featured standalone version (http://www.bitbucket.org/rfs/alvis) and its Sequence Bundles visualization module is further available as a web application (http://science-practice.com/projects/sequence-bundles).
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Registered trials
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