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

STAR Protocols (Mar 2022)

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

Affiliations

Xi Zhang: Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada; Institute for Comparative Genomics, Dalhousie University, Halifax, NS B3H 4R2, Canada; Corresponding author
Yining Hu: Department of Computer Science, Western University, London, ON N6A 5B7, Canada
Laura Eme: Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
Shinichiro Maruyama: Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
Robert J.M. Eveleigh: Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
Bruce A. Curtis: Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada; Institute for Comparative Genomics, Dalhousie University, Halifax, NS B3H 4R2, Canada
Shannon J. Sibbald: Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada; Institute for Comparative Genomics, Dalhousie University, Halifax, NS B3H 4R2, Canada
Julia F. Hopkins: Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
Gina V. Filloramo: Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada; Institute for Comparative Genomics, Dalhousie University, Halifax, NS B3H 4R2, Canada
Klaas J. van Wijk: Department of Plant Biology, Cornell University, Ithaca, NY 14853, USA
John M. Archibald: Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada; Institute for Comparative Genomics, Dalhousie University, Halifax, NS B3H 4R2, Canada; Corresponding author

Journal volume & issue: Vol. 3, no. 1
p. 101175

Abstract

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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).

Published in STAR Protocols

ISSN: 2666-1667 (Online)
Publisher: Elsevier
Country of publisher: United States
LCC subjects: Science: Science (General)
Website: https://star-protocols.cell.com/

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