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

在这个项目中，一组研究人员将开发新的算法和软件，同时对齐DNA序列和重建系统发育树。该方法和理论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。该项目将开发一种同时进行DNA序列比对和系统发育分析的方法，使研究人员能够克服这些问题。该项目的具体目标将是开发一个门户网站和开源软件，用于同时进行比对和系统发育分析，开发新的模拟器来模拟DNA序列进化，与组装生命之树（AToL）社区建立一个关于比对方法的工作组，并通过向少数民族机构开展外展活动，开发比对和系统发育估计的培训计划。该项目包括系统发育研究网络基础设施（CIPRES）项目的许多成员，并将为该数据资源提供重要的新分析能力。通过对非常大的数据集进行同步比对和系统发育分析，该项目将提供软件工具，为广泛的研究人员提供DNA序列数据的系统发育分析。这些工具将使考虑DNA区域的系统发育分析，不能对齐使用现有的工具。一个开源的门户接口将向更广泛的用户开放多个序列比对和树构建，现有AToL用户的参与将在软件开发过程的早期提供输入和评估。

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.