Continued development and maintenance of the PHAST software for comparative genomics

近年来，在全基因组测序方面投入了大量资金， 在生命之树上相互接近的物种，允许比较分析 前所未有的规模。这些分析主要依赖于严格的和 高效的计算工具。我们的Phylogenetic分析与空间/时间模型（PHAST） 软件包已经发展成为比较研究中使用最广泛的工具包之一， 基因组学PHAST包含流行的保护评分程序phastCons和phastP， 以及一个用于估计丰富的系统发育模型参数的程序，称为“系统发育拟合”， 以及众多的支持项目。我们已经开发和维护PHAST超过一年 十年来，它现在被成千上万的基因组研究人员使用。在此，我们建议继续 我们的工作是维护、改进和支持PHAST，并进行几项改进 需要PHAST跟上该领域的最新发展。我们的建议有两个 主要目标：（1）继续支持PHAST，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;以及（2） 扩展PHAST以支持具有数百到数千个基因组序列的新数据集， 更丰富、更通用的对齐表示。我们将密切协调发展， PHAST与UCSC基因组生物信息学小组在比对，可视化和 基因组重建我们的软件和浏览器曲目将继续免费提供给 研究社区。

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.