HyPhy: Molecular Evolutionary Analyses

HyPhy：分子进化分析

• 批准号: 8542870
• 负责人: Spencer V. Muse
• 金额: $ 26.51万
• 依托单位: NORTH CAROLINA STATE UNIVERSITY RALEIGH
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-09-15 至 2015-09-09
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8542870
• 关键词: Amino Acids; Animal Model; Area; Biomedical Research; Book Chapters; Classification; Code; Codon Nucleotides; Collection; Computer software; DNA; Data; Data Analyses; Development; Documentation; Drug resistance; Evolution; Funding; Gene Mutation; Genes; Genetic Programming; Genome; Genomics; Goals; Human; Immune response; Internet; Language; Libraries; Likelihood Functions; Machine Learning; Maintenance; Modeling; Molecular; Molecular Evolution; Molecular Sequence Data; Online Systems; Pathogenicity; Pattern; Peer Review; Performance; Phylogenetic Analysis; Phylogeny; Population; Procedures; Publications; RNA; Research Personnel; Resources; Software Engineering; Study models; System; Testing; Viral; Work; acronyms; base; combinatorial; comparative genomics; design; flexibility; improved; pathogen; pressure; programs; protein structure function; public health relevance; research study; tool; user-friendly; wiki

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.

描述（由申请人提供）：项目说明Hyphy（http://www.hyphy.org）是一个可脚本的软件平台，旨在在进化上下文中对DNA，RNA，密码子，氨基酸和其他类型的序列数据进行灵活而强大的分析。这种分析已成为大多数研究使用比较基因组数据的研究中必不可少的组成部分。生物学家和生物信息学家越来越认识到分子进化分析的益处。自2001年最初发行以来，Hyphy已成为一种相对稳定且成熟的产品，并已被4,500多名唯一用户下载，并将其集成到几个受欢迎的基于Web的基因组数据分析服务器中，并在400多个同行评审的出版物中引用并在三本书章节中进行了描述，尽管该章节的发展从来没有直接资助该包装。该提案寻求支持，以提高Hyphy系统的质量，性能，可靠性，模块化，文档和功能集。具体目标可以分为四个主要领域：1。软件工程，测试和文档的Hyphy Codebase。 2。用于系统发育最大似然模型拟合和推理的高性能发动机的开发。 3。在分子进化中用于机器学习应用的新发射的工具箱的扩展。 4。创建和维护Wiki主题文档资源。 公共卫生相关性：项目叙事分子进化分析对于基本，转化和应用生物医学研究的许多方面至关重要。例子包括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；估计人类或其他人群的进化相关性；表征基因或物种上选择性压力（自然或人造压力）的大小。