VEGA : visual comparison of phylogenetic trees for evolutionary genome analysis (ChinaVis 2019)

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2020
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Ge, Tong
Lu, Yonghua
Lu, Kecheng
Wang, Yunhai
Liu, Xin
Cheng, Zhanglin
Chen, Baoquan
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Journal of Visualization. Springer. 2020, 23(3), pp. 523-537. ISSN 1343-8875. eISSN 1875-8975. Available under: doi: 10.1007/s12650-020-00635-0
Zusammenfassung

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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ISO 690GE, Tong, Yonghua LU, Kecheng LU, Yunhai WANG, Xin LIU, Zhanglin CHENG, Yi CHEN, Oliver DEUSSEN, Baoquan CHEN, 2020. VEGA : visual comparison of phylogenetic trees for evolutionary genome analysis (ChinaVis 2019). In: Journal of Visualization. Springer. 2020, 23(3), pp. 523-537. ISSN 1343-8875. eISSN 1875-8975. Available under: doi: 10.1007/s12650-020-00635-0
BibTex
@article{Ge2020-06visua-49023,
  year={2020},
  doi={10.1007/s12650-020-00635-0},
  title={VEGA : visual comparison of phylogenetic trees for evolutionary genome analysis (ChinaVis 2019)},
  number={3},
  volume={23},
  issn={1343-8875},
  journal={Journal of Visualization},
  pages={523--537},
  author={Ge, Tong and Lu, Yonghua and Lu, Kecheng and Wang, Yunhai and Liu, Xin and Cheng, Zhanglin and Chen, Yi and Deussen, Oliver and Chen, Baoquan}
}
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