TreeTuner: A pipeline for minimizing redundancy and complexity in large phylogenetic datasets

STAR Protocols

Laura Eme¹  John M. Archibald²  Yining Hu²  Gina V. Filloramo²  Klaas J. van Wijk³  Robert J.M. Eveleigh³  Xi Zhang³  Bruce A. Curtis³  Julia F. Hopkins³  Shannon J. Sibbald³  Shinichiro Maruyama⁴ 

[1] Corresponding author;Institute for Comparative Genomics, Dalhousie University, Halifax, NS B3H 4R2, Canada;Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada;Department of Computer Science, Western University, London, ON N6A 5B7, Canada;

关键词: Bioinformatics;    Genomics;    Systems biology;    Evolutionary biology;   

DOI  :  

来源: DOAJ

【 摘 要 】

Summary: 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).

【 授权许可】

Unknown