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. Graphic abstract

中文翻译：

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VEGA：用于进化基因组分析的系统发育树的视觉比较 (ChinaVis 2019)

摘要 在进化基因组分析领域，生物学家试图通过比较系统发育树和分析基因座可能影响表型性状的突变来识别重要的基因或染色体区域。不幸的是，树比较和伴随的分析通常是手动执行的。在本文中，我们描述了进化基因组分析的工作流程，并对生物学家在分析过程中提出的基本问题进行了任务分析。我们提出了两种算法来实现定量树比较。一种是测量两棵树上对应的叶节点之间的差异，另一种是通过比较树结构与给定的生物分类来计算每个叶节点的分类不一致性。用获得的差异和不一致进行配置，我们提出了一个可视化分析系统，用于进化基因组分析的系统发育树的可视化比较，它不仅使生物学家能够直观地探索树木，还可以通过比较所选叶节点的 SNP 变体来识别影响其性状的基因座。我们以两位生物学家的案例研究结束，他们使用我们的系统来增强他们以前的手动分析工作流程，并证明我们的系统可以揭示更多的洞察力。图形摘要 我们以两位生物学家的案例研究结束，他们使用我们的系统来增强他们以前的手动分析工作流程，并证明我们的系统可以揭示更多的洞察力。图形摘要 我们以两位生物学家的案例研究结束，他们使用我们的系统来增强他们以前的手动分析工作流程，并证明我们的系统可以揭示更多的洞察力。图形摘要