Continued development and maintenance of the PHAST software for comparative genomics

持续开发和维护用于比较基因组学的 PHAST 软件

• 批准号: 9058580
• 负责人: Adam Charles Siepel
• 金额: $ 19.2万
• 依托单位: COLD SPRING HARBOR LABORATORY
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-04-24 至 2018-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9058580
• 关键词: Acceleration; Address; Area; Arthropods; Bioinformatics; Code; Communities; Comparative Genomic Analysis; Complex; Computer software; Computing Methodologies; Data Set; Development; Documentation; Elements; Environment; Eukaryota; Fellowship; Funding; Genome; Genomics; Grant; Human; Human Genetics; Imagery; Insecta; Investments; Life; Maintenance; Mammals; Manuals; Measures; Modeling; Molecular; Molecular Biology; Molecular Evolution; Phylogenetic Analysis; Process; Production; Publications; Research; Research Personnel; Resources; System; Testing; Time; Trees; Update; Vertebrates; Work; comparative; comparative genomics; computerized tools; falls; genome browser; genome sequencing; genomic data; improved; insight; novel; programs; reconstruction; software development; tool; vertebrate genome; web interface; whole genome

In recent years, there have been enormous investments in complete genome sequencing of species that fall close to one another on the tree of life, to permit comparative analyses on unprecedented scales. These analyses depend critically on the existence of rigorous and efficient computational tools. Our PHylogenetic Analysis with Space/Time models (PHAST) software package has developed into one of the most widely used toolsets in comparative genomics. PHAST contains the popular conservation scoring programs phastCons and phyloP, as well as a program for estimating the parameters of rich phylogenetic models, called phyloFit, and numerous supporting programs. We have developed and maintained PHAST for over a decade and it is now used by thousands of genomic researchers. Here we propose to continue our work maintaining, improving, and supporting PHAST, and to make several improvements needed for PHAST to keep abreast of recent developments in the field. Our proposal has two main aims: (1) to continue maintenance of support of PHAST, to make various improvements to our software development process, and to improve the accessibility of the software; and (2) to extend PHAST to support new data sets with hundreds to thousands of genome sequences and richer, more general alignment representations. We will closely coordinate our development of PHAST with the UCSC Genome Bioinformatics group's efforts on alignment, visualization, and genome reconstruction. Our software and browser tracks will remain freely available to the research community.

近年来，在完整的基因组测序中进行了巨大的投资 在生命树上彼此接近的物种，以允许对 前所未有的量表。这些分析急于严格和 有效的计算工具。我们使用空间/时间模型（PHAST）的系统发育分析 软件包已发展为比较中使用最广泛的工具集之一 基因组学。 Phast包含流行的保护评分计划Phastcons和Phylop， 以及一个用于估算丰富的系统发育模型参数的程序，称为Thylofit， 以及许多支持计划。我们已经开发并维护了 十年，现在已被数千名基因组研究人员使用。在这里我们建议继续 我们的工作维持，改进和支持PHAST，并做出一些改进 Phast需要与该领域的最新发展保持一致。我们的建议有两个 主要目的：（1）继续维持PHAST的支持，以进行各种改进 我们的软件开发过程，并提高软件的可访问性； （2）到 扩展PHAST以支持数百至数千个基因组序列的新数据集，并且 更丰富，更一般的一致性表示。我们将密切协调我们的发展 Phast与UCSC基因组生物信息学小组在对齐，可视化和 基因组重建。我们的软件和浏览器轨道将保持自由 研究社区。