Treetrimmer: A method for phylogenetic dataset size reduction

Shinichiro Maruyama, Robert Jm Eveleigh, John M. Archibald

Research output: Contribution to journalArticlepeer-review

15 Citations (Scopus)

Abstract

Background: With rapid advances in genome sequencing and bioinformatics, it is now possible to generate phylogenetic trees containing thousands of operational taxonomic units (OTUs) from a wide range of organisms. However, use of rigorous tree-building methods on such large datasets is prohibitive and manual 'pruning' of sequence alignments is time consuming and raises concerns over reproducibility. There is a need for bioinformatic tools with which to objectively carry out such pruning procedures. Findings. Here we present 'TreeTrimmer', a bioinformatics procedure that removes unnecessary redundancy in large phylogenetic datasets, alleviating the size effect on more rigorous downstream analyses. The method identifies and removes user-defined 'redundant' sequences, e.g., orthologous sequences from closely related organisms and 'recently' evolved lineage-specific paralogs. Representative OTUs are retained for more rigorous re-analysis. Conclusions: TreeTrimmer reduces the OTU density of phylogenetic trees without sacrificing taxonomic diversity while retaining the original tree topology, thereby speeding up downstream computer-intensive analyses, e.g., Bayesian and maximum likelihood tree reconstructions, in a reproducible fashion.

Original languageEnglish
Article number145
JournalBMC Research Notes
Volume6
Issue number1
DOIs
Publication statusPublished - 2013
Externally publishedYes

Keywords

  • Dereplication
  • Phylogenetic tree
  • Pruning
  • Taxonomic category
  • TreeTrimmer

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

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