Abstract
Phylogenetic trees are used by researchers across multiple fields of study to display historical relationships between organisms or genes. Trees are used to examine the speciation process in evolutionary biology, to classify families of viruses in epidemiology, to demonstrate co-speciation in host and pathogen studies, and to explore genetic changes occurring during the disease process in cancer, among other applications. Due to their complexity and the amount of data they present in visual form, phylogenetic trees have generally been difficult to render for publication and challenging to directly interact with in digital form. To address these limitations, we developed PhyloPen, an experimental novel multi-touch and pen application that renders a phylogenetic tree and allows users to interactively navigate within the tree, examining nodes, branches, and auxiliary information, and annotate the tree for note-taking and collaboration. We present a discussion of the interactions implemented in PhyloPen and the results of a formative study that examines how the application was received after use by practicing biologists -- faculty members and graduate students in the discipline. These results are to be later used for a fully supported implementation of the software where the community will be welcomed to participate in its development.
Highlights
Phylogenetic trees are a visual representation of the hierarchical relationships of common descent among a set of species or genes from a common ancestor
Many existing tree rendering packages, such as FigTree, Mesquite, and others used by phylogenetics experts today, generate static renderings of tree diagrams
Phylogenetic trees output from analysis programs (e.g. BEAST and Mr Bayes) almost always have to be stylistically altered before presentation and/or publication, with branches colored and rotated, annotations added, and tip labels changed for readability
Summary
Phylogenetic trees are a visual representation of the hierarchical relationships of common descent among a set of species or genes from a common ancestor Often, these diagrams include branch lengths to provide a time scale of the divergence of species or genes from their common ancestor. Experts sometimes have to resort to manually adjusting the diagrams themselves using image editing software, such as Adobe Illustrator, which is a process that can be very time consuming. For these reasons, the goal of our work-in-progress application is to provide biology experts with an interactive experience that is efficient and hopefully more natural to use than existing tools. A unique contribution of this work is that it brings together the technologies of pen, touch, and annotation in a single system
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