Algorithms and Software for Phylogenetic Supertrees

系统发育超级树的算法和软件

• 批准号: 0075319
• 负责人: Michael Sanderson
• 金额: $ 37万
• 依托单位: University of California-Davis
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2000
• 资助国家: 美国
• 起止时间: 2000-10-01 至 2004-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0075319&HistoricalAwards=false
• 关键词: Algorithms; Software; Phylogenetic; Supertrees

0075319Sanderson and Gusfield Supertrees are phylogenies (rooted evolutionary trees) assembled from smaller phylogenies that share some but not all taxa (twigs or end branches) in common. Thus, supertrees can make novel statements about relationships of taxa that do not co-occur on any single source tree while still retaining all the hierarchical information from all source trees. As a method of combining existing phylogenetic information, supertrees potentially solve many of the problems incurred by other methods, such as lack of homologous characters, incompatible data types, or combining trees with different taxa. However, despite the potential for constructing large trees and synthesizing phylogenetic relationships from trees based on disparate sources of evidence, supertree construction has mainly been an informal "by hand" operation, done without the use of specially developed software. Furthermore, there is little ground for assessing the reliability of such supertrees. In a collaboration among biologists and computer scientists, Drs. Sanderson, Gusfield, and colleagues are examining a new class of methods that is somewhat analogous to phylogenetic distance methods but uses a novel distance measure based on "flips" of cells in the matrix representation of the source trees. In addition to generating supertrees, flip-supertree methods will help systematists focus on poorly known or contentious taxa, thereby directing future systematic effort where it is most needed. Accuracy and speed of supertree methods will be tested through simulation studies, and through use of the web-based database of phylogenetic trees in TreeBASE, to determine methods most useful to systematists. The graphically oriented software to be developed will implement various supertree algorithms and offer improved methods to visualize and compare trees that share some, but not all, taxa in common.

0075319桑德森和格斯菲尔德超级树是由共享一些但不是所有分类群（细枝或末端分支）的较小的进化树组装而成的进化树（有根进化树）。因此，超树可以对分类群的关系做出新的陈述，这些关系不会在任何单个源树上共同出现，同时仍然保留来自所有源树的所有层次信息。作为一种结合已有系统发育信息的方法，超树可能解决其他方法所带来的许多问题，如缺乏同源特征，不兼容的数据类型，或将不同分类群的树结合起来。然而，尽管有潜力构建大型树木和综合系统发育关系的树木的基础上不同的证据来源，超级树的建设主要是一个非正式的“手工”操作，没有使用专门开发的软件。此外，几乎没有理由评估这种超级树的可靠性。在生物学家和计算机科学家之间的合作中，Sanderson博士，Gusfield及其同事正在研究一类新的方法，该方法有点类似于系统发育距离方法，但使用了一种基于源树矩阵表示中细胞的“翻转”的新型距离度量。除了生成超级树，翻转超级树方法将帮助系统学家专注于鲜为人知或有争议的分类群，从而将未来的系统工作导向最需要的地方。超树方法的准确性和速度将通过模拟研究进行测试，并通过使用TreeBASE中基于网络的系统发生树数据库，以确定对系统学家最有用的方法。将开发的图形化软件将执行各种超树算法，并提供改进的方法来可视化和比较共享一些但不是所有共同分类群的树木。