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04-03-2020 | Regular Paper | Issue 3/2020

Journal of Visualization 3/2020

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

Journal:
Journal of Visualization > Issue 3/2020
Authors:
Tong Ge, Yonghua Lu, Kecheng Lu, Yunhai Wang, Xin Liu, Zhanglin Cheng, Yi Chen, Oliver Deussen, Baoquan Chen
Important notes
Tong Ge and Yonghua Lu assert equal contribution and joint first authorship.

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Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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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