ArticleBMC bioinformatics2025
VIRI: a visualization tool for tree reconciliations.
Article in BMC bioinformatics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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4 authors.
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Abstract
backgroundCophylogeny reconciliation is a powerful method for analyzing host-symbiont coevolution. The cophylogeny problem consists of mapping the phylogenetic tree of the symbionts into the one of the hosts, including events such as duplications, co-speciation, host-switches, and extinctions by comparing the discrepancies between the topologies of the associated symbiont evolutionary trees. Visualizing tree reconciliations is important for biologists as it aids in understanding and identifying specific patterns in the coevolution of hosts and symbionts. Additionally, when multiple optimal solutions exist, it allows for the quick comparison of different reconciliations between the same pair of trees.
resultsHere, we present VIRI (visual inspector of reconciliation instances), a new tree reconciliation visualizer. We adopt a hybrid metaphor combining space-filling (for host trees) and node-link (for symbiont trees) approaches, implementing the algorithms described in Calamoneri et al. (Theor Comput Sci 815:228-245. https://doi.org/10.1016/j.tcs.2019.12.024 , 2020). The visualizations produced by VIRI are designed to be clear and interpretable, thanks to an unambiguous, top-down layout of tree reconciliations and the preservation of the user's mental map when comparing multiple reconciliations on the same pair of trees. In particular, the consistent use of a shared host tree layout across visualizations is a novel feature that facilitates direct comparison. Moreover, VIRI proposes a crossing-free visualization whenever possible. Finally, VIRI allows users to store datasets and download their visualizations, offering a convenient way to organize and share data. An example of visualization produced by VIRI is depicted in Fig. 1.
conclusionsVIRI efficiently produces clear and easy-to-read visualizations of tree reconciliations. VIRI is free and available at https://viri.di.uniroma1.it/ .
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.