PhyloTraVis: A New Approach to Visualization of the Phylogenetic Tree

The study of evolution is an essential task in predicting the variability of species, especially for pathogens such as viruses. One of the main stages of evolutionary analysis is constructing a phylogenetic tree. This work is devoted to developing a new approach for visualization of the phylogenetic...

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Bibliographic Details
Published in:Programming and computer software 2022-06, Vol.48 (3), p.215-226
Main Authors: Forghani, M., Vasev, P. A., Bolkov, M. A., Ramsay, E. S., Bersenev, A. Y.
Format: Article
Language:English
Subjects:
Algorithms
Amino acids
Artificial Intelligence
Bioinformatics
Change detection
Computer Science
Evolution
Genomes
Influenza
Mutation
Operating Systems
Pathogens
Phylogenetics
Software Engineering
Software Engineering/Programming and Operating Systems
Trajectories
Vaccines
Viruses
Visualization
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Summary:The study of evolution is an essential task in predicting the variability of species, especially for pathogens such as viruses. One of the main stages of evolutionary analysis is constructing a phylogenetic tree. This work is devoted to developing a new approach for visualization of the phylogenetic tree, which is based on reconstructing the evolutionary trajectory of a taxon in three-dimensional space. An evolutionary trajectory is a path that connects a particular taxon and the root of the tree. By reconstructing ancestral sequences and applying one-hot-encoding, each tree node is represented as a multidimensional object, then mapped into three-dimensional space using the embedding method, due to which, evolutionary paths from leaves to the tree’s root are generated. This approach makes it possible to visualize rapid changes in evolutionary direction, both locally and globally. The results are based on the experiments on visualization of the evolutionary trajectory of the H3N2 influenza virus and the development of a publicly available web platform called PhyloTraVis. They suggest the application of our approach for early detection of changes in the direction of evolution, the study of evolutionary dynamics, evaluation of emerging novel virus variants, and modeling of possible antigenic diversity, which are important tasks in computational virology.
ISSN:0361-7688
1608-3261
DOI:10.1134/S0361768822030045