title: Treetrimmer: a method for phylogenetic dataset size reduction.
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.
  
  
  RESULTS
  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.
authors.affiliation: Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, Canada.
authors.forename: Shinichiro
authors.initials: S
authors.lastname: Maruyama
authors.forename: Robert J M
authors.initials: RJ
authors.lastname: Eveleigh
authors.forename: John M
authors.initials: JM
authors.lastname: Archibald
mesh_terms: D000465:Algorithms; D001331:Automation; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D003576:Electron Transport Complex IV / Q000235:genetics; D016247:Information Storage and Retrieval; D010802:Phylogeny; D011336:Probability; D000461:Rhodophyta / Q000235:genetics; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D003576:Electron Transport Complex IV