III-CTX: Large-Scale Analysis of Collections of Phylogenetic Trees

系统发育分析的目的是建立一个描述生物体（或分类群）之间亲缘关系的进化树。推断出一个系统发育树，代表了一个很好的假设的真相是一个困难的问题。系统发生树学试图在指数大小的树空间中搜索非常小的一部分，以获得真正进化树的良好近似。拟议的研究项目的总体目标是开发信息丰富的方法，用于分析在系统发育搜索过程中遇到的大量树木。对搜索行为的更好理解可以推动更好的系统发育学的设计，最终导致更准确的系统发育树重建。具体的研究目标包括：（一）开发一个搜索历史存储库，其中包含所有的树检查的系统发育启发式;（二）设计算法，利用信息模式的搜索历史存储库;和（三）开发可视化工具，提供信息视图的数据驻留在存储库中。 为该研究项目开发的新数据分析和可视化技术将补充现有的NSF资助的努力，以建立诸如“生命之树”的所有已知生物的进化史。此外，拟议的工作将为不同的学生群体提供指导和跨学科培训。

Given a collection of organisms (or taxa), the objective of a phylogenetic analysis is to produce an evolutionary tree describing the genealogical relationships between the taxa. Inferring a phylogenetic tree that represents a good hypothesis of the truth is a difficult problem. Phylogenetic heuristics attempt to search a very small fraction of the exponentially-sized tree space for good approximations of the true evolutionary tree. The overall goal of the proposed research project is to develop information-rich methods for analyzing the large collection of trees encountered during a phylogenetic search. A better understanding of search behavior can drive the design of better heuristics, which ultimately lead to more accurate reconstructions of phylogenetic trees. Specific research objectives include: (i) developing a search history repository that contains all of the trees examined by a phylogenetic heuristic; (ii) designing algorithms for exploiting informative patterns in a search history repository; and (iii) developing visualization tools that provide informative views of the data residing in the repository. The novel data analysis and visualization techniques developed for this research project will complement existing NSF-funded efforts to build phylogenies such as "The Tree of Life", the evolutionary history of all known organisms. Moreover, the proposed work will provide mentoring and interdisciplinary training to a diverse group of students.