Abstract
In the field of evolutionary genome analysis, biologists seek to identify important genes or chromosome regions by comparing phylogenetic trees and analyzing the mutation at which locus might affect phenotypic traits. Unfortunately, the tree comparison and accompanying analysis are often performed manually. In this paper, we characterize the workflow of evolutionary genome analysis and present a task analysis for the fundamental questions asked by biologists during the analysis procedure. We propose two algorithms to enable quantitative tree comparison. One is to measure the differences between corresponding leaf nodes on two trees, and the other is to compute the classification inconsistency of each leaf node by comparing tree structure with a given biological classification. Configuring with the obtained difference and inconsistency, we present a visual analysis system, visual comparison of phylogenetic trees for evolutionary genome analysis, which not only enables biologists to intuitively explore trees but also identify locus which affects their traits by comparing SNP variants of selected leaf nodes. We conclude with case studies from two biologists who used our system to augment their previous manual analysis workflow and demonstrate that our system can reveal more insight.
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Acknowledgements
This work is supported by the Grants of NSFC (61772315, 61602273), Shenzhen Science and Technology Program (JSGG20170412170711532) and the Open Research Fund of Beijing Key Laboratory of Big Data Technology for Food Safety, Beijing Technology and Business University (BKBD-2017KF02).
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Ge, T., Lu, Y., Lu, K. et al. VEGA: visual comparison of phylogenetic trees for evolutionary genome analysis (ChinaVis 2019). J Vis 23, 523–537 (2020). https://doi.org/10.1007/s12650-020-00635-0
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DOI: https://doi.org/10.1007/s12650-020-00635-0