Collaborative Research: Large-scale simultaneous multiple alignment and phylogeny estimation

合作研究：大规模同时多重比对和系统发育估计

基本信息

批准号：
0733029
负责人：
Tandy Warnow
金额：
$ 159.03万
依托单位：
University of Texas at Austin
依托单位国家：
美国
项目类别：
Continuing Grant
财政年份：
2007
资助国家：
美国
起止时间：
2007-10-01 至 2014-09-30
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=0733029&HistoricalAwards=false
关键词：
Collaborative Research Large scale simultaneous

项目摘要

In this project, a team of investigators will develop new algorithms and software to simultaneously align DNA sequences and reconstruct phylogenetic trees. This methods and theory-oriented project addresses an important problem in phylogenetic reconstruction: relatively poor performance of existing tools in the face of insertions, deletions, and duplications in large datasets. This project will develop a simultaneous approach to DNA sequence alignment and phylogenetic analysis that will allow researchers to overcome these problems. Specific goals for the project will be to develop a portal and open-source software for simultaneous alignment and phylogenetic analysis, develop new simulators to model DNA sequence evolution, establish a working group on alignment methods with the Assembling the Tree of Life (AToL) community, and develop training programs in alignment and phylogeny estimation with outreach activities to minority institutions. The project includes many members of the Cyberinfrastructure for Phylogenetic Research (CIPRES) project and will provide significant new analytic capabilities for that data resource. By making simultaneous alignment and phylogenetic analysis feasible for very large datasets, this project will provide software tools that will serve a broad community of researchers conducting phylogenetic analyses of DNA sequence data. These tools will enable consideration of DNA regions for phylogenetic analysis that cannot be aligned using existing tools. An open-source, portal interface will open multiple sequence alignment and tree-building to a broader range of users and engagement of existing AToL users will provide input and evaluation early in the software development process.

在这个项目中，一组研究人员将开发新的算法和软件，以同时对齐DNA序列并重建系统发育树。这种方法和以理论为导向的项目解决了系统发育重建中的一个重要问题：面对大型数据集中的插入，删除和重复，现有工具的性能相对较差。该项目将开发出一种同时的DNA序列比对和系统发育分析的方法，这将使研究人员能够克服这些问题。该项目的具体目标是开发一个门户和开源软件，用于同时对齐和系统发育分析，开发新的模拟器来建模DNA序列演变，建立一个与群落（ATOL）社区组装的对齐方式的工作组，并在对齐方面开发培训计划，并在对次要活动中开发培训计划，并将其与临近活动进行估算。该项目包括用于系统发育研究（CIPRES）项目的网络基础架构的许多成员，并将为该数据资源提供重要的新分析能力。通过使非常大的数据集的同时对齐和系统发育分析可行，该项目将提供软件工具，这些工具将服务于进行DNA序列数据的系统发育分析的广泛研究人员社区。这些工具将使您可以考虑使用现有工具对齐的系统发育分析的DNA区域。开源的门户接口将为更广泛的用户打开多个序列对齐和树木建造，现有ATOL用户的参与度将在软件开发过程的早期提供输入和评估。