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，以同时比对DNA序列并重建系统发育树。这个以方法和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用于同时比对和系统发育分析的门户和开放源码软件，开发新的模拟器来模拟DNA序列进化，与组装生命树(ATOL)社区建立一个比对方法工作组，并通过与少数族裔机构的外联活动制定比对和系统发育评估培训方案。该项目包括数字系统发育研究基础设施(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。通过使超大型数据集的同时比对和系统发生分析成为可能，该项目将提供软件工具，为进行DNA序列数据系统发生分析的广大研究人员提供服务。这些工具将使人们能够考虑用现有工具无法比对的DNA区域进行系统发育分析。开源的门户界面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投入和评估。

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.