Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada.
Institute for Comparative Genomics, Dalhousie University, Halifax, NS B3H 4R2, Canada.
STAR Protoc. 2022 Feb 15;3(1):101175. doi: 10.1016/j.xpro.2022.101175. eCollection 2022 Mar 18.
Various bioinformatics protocols have been developed for trimming the number of operational taxonomic units (OTUs) in phylogenetic datasets, but they typically require significant manual intervention. Here we present TreeTuner, a semiautomated pipeline that allows both coarse and fine-scale tuning of large protein sequence phylogenetic datasets via the minimization of OTU redundancy. TreeTuner facilitates preliminary investigation of such datasets as well as more rigorous downstream analysis of specific subsets of OTUs. For complete details on the use and execution of this protocol, please refer to Maruyama et al. (2013) and Sibbald et al. (2019).
已经开发了各种生物信息学协议来修剪系统发育数据集的操作分类单元（OTUs）数量，但它们通常需要大量的手动干预。在这里，我们展示了 TreeTuner，这是一个半自动化的管道，通过最小化 OTU 冗余，可以对大型蛋白质序列系统发育数据集进行粗调和细调。TreeTuner 有助于对这些数据集进行初步研究，以及对特定 OTU 子集进行更严格的下游分析。有关此协议的使用和执行的完整详细信息，请参阅 Maruyama 等人（2013 年）和 Sibbald 等人（2019 年）。
