Ecology, Evolution, and Marine Biology, University of California-Santa Barbara, Santa Barbara, CA 93106, USA.
BMC Bioinformatics. 2014 Jul 2;15:230. doi: 10.1186/1471-2105-15-230.
Phylogenetic tools and 'tree-thinking' approaches increasingly permeate all biological research. At the same time, phylogenetic data sets are expanding at breakneck pace, facilitated by increasingly economical sequencing technologies. Therefore, there is an urgent need for accessible, modular, and sharable tools for phylogenetic analysis.
We developed a suite of wrappers for new and existing phylogenetics tools for the Galaxy workflow management system that we call Osiris. Osiris and Galaxy provide a sharable, standardized, modular user interface, and the ability to easily create complex workflows using a graphical interface. Osiris enables all aspects of phylogenetic analysis within Galaxy, including de novo assembly of high throughput sequencing reads, ortholog identification, multiple sequence alignment, concatenation, phylogenetic tree estimation, and post-tree comparative analysis. The open source files are available on in the Bitbucket public repository and many of the tools are demonstrated on a public web server (http://galaxy-dev.cnsi.ucsb.edu/osiris/).
Osiris can serve as a foundation for other phylogenomic and phylogenetic tool development within the Galaxy platform.
系统发生工具和“树思维”方法越来越渗透到所有的生物学研究中。与此同时，由于测序技术越来越经济实惠，系统发生数据集也在以惊人的速度扩张。因此，迫切需要可访问、模块化和可共享的系统发生分析工具。
我们为 Galaxy 工作流管理系统开发了一套新的和现有的系统发生工具的包装器，我们称之为 Osiris。Osiris 和 Galaxy 提供了一个可共享、标准化、模块化的用户界面，以及使用图形界面轻松创建复杂工作流程的能力。Osiris 使 Galaxy 中的系统发生分析的各个方面都成为可能，包括高通量测序reads 的从头组装、同源基因识别、多重序列比对、串联、系统发生树估计和树后比较分析。开源文件可在 Bitbucket 公共存储库中获得，并且许多工具都在公共 Web 服务器（http://galaxy-dev.cnsi.ucsb.edu/osiris/）上进行了演示。
Osiris 可以作为 Galaxy 平台内其他系统发生组学和系统发生工具开发的基础。
