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

Xi Zhang, Yining Hu, Laura Eme, Shinichiro Maruyama, Robert J.M. Eveleigh, Bruce A. Curtis, Shannon J. Sibbald, Julia F. Hopkins, Gina V. Filloramo, Klaas J. van Wijk, John M. Archibald

Research output: Contribution to journalArticlepeer-review


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).

Original languageEnglish
Article number101175
JournalSTAR Protocols
Issue number1
Publication statusPublished - 2022 Mar 18
Externally publishedYes


  • Bioinformatics
  • Evolutionary biology
  • Genomics
  • Systems biology

ASJC Scopus subject areas

  • Neuroscience(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)


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