HyPhy: Molecular Evolutionary Analyses

项目描述(由申请人提供)：项目描述Hyphy(http://www.hyphy.org)是一个可编写脚本的软件平台，旨在灵活而强大地分析进化背景下的脱氧核糖核酸、核糖核酸、密码子、氨基酸和其他类型的序列数据。这种分析已经成为利用比较基因组数据的大多数研究研究中不可或缺的组成部分。生物学家和生物信息学家越来越认识到分子进化分析的好处。自2001年首次发布以来，HYPHY已成为一个相对稳定和成熟的产品，已被4,500多个独立用户下载，集成到几个流行的基于网络的基因组数据分析服务器中，被400多种同行评议的出版物引用，并在三本书的章节中描述，尽管该软件包的开发从未得到直接资助。这项提议寻求支持，以改进HYPHY系统的质量、性能、可靠性、模块化、文件和功能集。具体目标可以分为四个主要领域：1.软件工程、测试和hyphy代码库的文档编制。2.高性能系统发育极大似然模型拟合推理机的研制。3.扩展了一个新启动的工具箱，用于分子进化中的机器学习应用。4.创建和维护以维基为主题的文件资源。 公共卫生相关性：项目叙述分子进化分析是基础、翻译和应用生物医学研究的许多方面的中心。例如，识别允许病原体逃避免疫反应的基因突变；预测蛋白质的结构和功能；估计人类或其他种群的进化关联性；表征对基因或物种的选择压力的大小，无论是自然的还是人为的。

DESCRIPTION (provided by applicant): Project Description HyPhy (http://www.hyphy.org) is a scriptable software platform designed to enable flexible and powerful analyses of DNA, RNA, codon, amino acid and other types of sequence data in an evolutionary context. Such analyses have become an indispensable component of most research studies that make use of comparative genomic data. Biologists and bioinformaticians increasingly recognize the benefits of molecular evolutionary analyses. Since its initial release in 2001, HyPhy has become a relatively stable and mature product, and has been downloaded by more than 4,500 unique users, integrated into several popular web-based genomic data analysis servers, cited in over 400 peer-reviewed publications and described in three book chapters, in spite of the fact that the development of the package has never been directly funded. This proposal seeks support to improve the quality, performance, reliability, modularity, documentation and feature sets of the HyPhy system. Specific aims can be divided into four major areas: 1. Software engineering, testing, and documentation of the HyPhy codebase. 2. The development of a high-performance engine for phylogenetic maximum likelihood model fitting and inference. 3. Extension of a newly-initiated toolbox for machine learning applications in molecular evolution. 4. Creation and maintenance of a wiki-themed documentation resource. PUBLIC HEALTH RELEVANCE: Project Narrative Molecular evolutionary analyses are central to many aspects of basic, translational, and applied biomedical research. Examples include identifying gene mutations that allow pathogens to evade the immune response; prediction of the structure and function of proteins; estimating the evolutionary relatedness of human or other populations; characterizing the magnitude of selective pressure, either natural or artificial, on genes or species.