ABI Development: Computational infrastructure for phylogenetic analysis in the R environment

在过去的几十年里，系统发育树，即用来表示基因序列、种群或物种之间的祖先-后代关系的图，已经成为越来越广泛的生物学学科如生态学、进化生物学、分子生物学、比较基因组学和发育科学研究中不可或缺的一部分。系统发育学也开始在生物学之外的不同研究领域，如比较语言学、人类学和法医学中得到应用。与此同时，被称为R的计算环境已经发展成为科学计算的领先平台之一。R的优势来自于由计算科学家和非R核心开发团队成员的计算科学家和开发人员免费开发和分发的数千个贡献的函数库(称为“包”)。由于这些贡献，R已经成长为操纵、可视化和分析系统发育树的卓越软件平台。尽管如此，从R的数据中实际估计系统发育树的能力仍然相对有限。这一奖项的主要目标是大幅扩展可用于在R科学计算环境中进行系统发育评估的工具包。该工具包将采用开放发展模式制作，并将作为免费和开放源码的资源分发给国家和国际科学界。在R中开发用于科学计算的软件的主要优势之一是，通过允许将数据分析管道的所有阶段构建成来自开源组件的单一的、完全可重现的工作流程，这样做极大地促进了科学的重现性。这项研究将创建新的、开源的、自由分布的软件工具，将在整个系统发育科学界和更远的地方广泛使用。总的目标是R的系统发育的计算基础设施的发展。这些研究人员将特别侧重于四个具体目标：(1)计算树之间距离的方法的开发和应用；(2)新的共识和平均树方法的开发；(3)基于可能性的物种-树联合估计方法的开发；以及，最后，(4)树集合和系统发育网络可视化工具的应用。他们特别关注这些研究目标，因为它们以特别有趣的方式相互作用，因为它们反映了需要进行实质性研究的领域；然而，对这些主题的研究可能会在根本上新的领域产生意想不到的发现。该奖项还将支持博士后和研究生培训，后者通过面向年轻开发人员的密集、系统学方法新兵训练营。开展这一培训目标的目的是帮助形成下一代计算系统发育生物学家，并将面向传统上在科学界代表性较低的群体的研究生参加。该项目的系统发育工具将托管在CRAN at https://cran.r-project.org/web/packages/phytools/index.htmlThis，该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

Over the past several decades, phylogenetic trees, the graphs that are used to represent the ancestor-descendant relationships between gene sequences, populations, or species, have become integral in scientific research across an increasingly widening range of biological disciplines such as ecology, evolutionary biology, molecular biology, comparative genomics, and development. Phylogenies too have begun to see application outside of biology in such diverse fields of study as comparative linguistics, anthropology, and forensic science. Meanwhile, the computational environment known as 'R' has developed into one of the leading platforms for scientific computing. The strength of R comes from the literally thousands of contributed function libraries (called "packages") developed and distributed for free by computational scientists and developers that are not members of the R core development team. Because of these contributions, R has grown into the preeminent software platform for manipulating, visualizing, and analyzing phylogenetic trees. That said, the capability to actually estimate phylogenetic trees from data in R remains relatively limited. The major objective of this award is to substantially extend the toolkit that is available to undertake phylogeny estimation in the R scientific computing environment. This toolkit will be built using an open development model and will be distributed as a free and open-source resource to the national and international scientific communities. Among the major advantages of developing software for scientific computing in R is that so doing dramatically facilitates scientific reproducibility by allowing all stages of the data analysis pipeline to be built into a single, fully reproducible workflow from open source components.This research will create new, open-source, and freely distributed software tools that will be of broad utility throughout the phylogenetic scientific community and beyond. The general goal is computational infrastructure development for phylogenetics in R. These investigators will focus on four specific objectives in particular: (1) the development and application of methods to compute distances between trees; (2) the development of new consensus and average tree methods; (3) the development of joint species-tree estimation methods based on likelihood; and, finally, (4) the application of visualization tools for sets of trees and phylogenetic networks. They focus specifically on these research objectives because they interact in particularly interesting ways and because they reflect areas in which substantial research is needed; however, research on these topics will likely result in unanticipated discoveries in fundamentally new areas. The award will also support postdoctoral and graduate training, the latter via an intensive, phylogeny methods boot camp for young developers. This training objective will be undertaken with the aim of helping to form the next generation of computational phylogenetic biologists and will target for participation graduate students from groups traditionally underrepresented in the sciences. Phylogenetic tools from this project will be hosted on the CRAN at https://cran.r-project.org/web/packages/phytools/index.htmlThis award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.