DeBlasio Dan F, Wisecaver Jennifer H
Department of Computer Science, University of Arizona , Tucson , AZ , United States.
Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, United States.
PeerJ. 2016 Aug 23;4:e2359. doi: 10.7717/peerj.2359. eCollection 2016.
We present the phylogeny analysis software SICLE (Sister Clade Extractor), an easy-to-use, high-throughput tool to describe the nearest neighbors to a node of interest in a phylogenetic tree as well as the support value for the relationship. The application is a command line utility that can be embedded into a phylogenetic analysis pipeline or can be used as a subroutine within another C++ program. As a test case, we applied this new tool to the published phylome of Salinibacter ruber, a species of halophilic Bacteriodetes, identifying 13 unique sister relationships to S. ruber across the 4,589 gene phylogenies. S. ruber grouped with bacteria, most often other Bacteriodetes, in the majority of phylogenies, but 91 phylogenies showed a branch-supported sister association between S. ruber and Archaea, an evolutionarily intriguing relationship indicative of horizontal gene transfer. This test case demonstrates how SICLE makes it possible to summarize the phylogenetic information produced by automated phylogenetic pipelines to rapidly identify and quantify the possible evolutionary relationships that merit further investigation. SICLE is available for free for noncommercial use at http://eebweb.arizona.edu/sicle/.
我们展示了系统发育分析软件SICLE（姐妹进化枝提取器），这是一个易于使用的高通量工具，用于描述系统发育树中感兴趣节点的最近邻以及该关系的支持值。该应用程序是一个命令行实用程序，可以嵌入到系统发育分析管道中，也可以作为另一个C++程序中的子例程使用。作为一个测试案例，我们将这个新工具应用于已发表的嗜盐拟杆菌属物种盐红菌的系统发育组，在4589个基因系统发育中确定了与盐红菌的13种独特姐妹关系。在大多数系统发育中，盐红菌与细菌聚在一起，大多数情况下是其他拟杆菌，但有91个系统发育显示盐红菌与古菌之间存在分支支持的姐妹关联，这是一种在进化上引人关注的关系，表明了水平基因转移。这个测试案例展示了SICLE如何能够总结自动化系统发育管道产生的系统发育信息，以快速识别和量化值得进一步研究的可能进化关系。SICLE可在http://eebweb.arizona.edu/sicle/免费用于非商业用途。
