Ge-specific paralogs. Representative OTUs are retained for much more rigorous re-analysis. Conclusions: TreeTrimmer reduces the OTU density of phylogenetic trees with out sacrificing taxonomic diversity although retaining the original tree topology, thereby speeding up downstream computer-intensive analyses, e.g., Bayesian and maximum likelihood tree reconstructions, inside a reproducible style. Keyword phrases: TreeTrimmer, Phylogenetic tree, Pruning, Dereplication, Taxonomic categoryBackground Molecular phylogeny is actually a strong tool for inferring evolutionary relationships. With advances in high-throughput genome and transcriptome sequencing it really is now feasible to construct trees from nucleic acid and protein sequence alignments containing a huge number of OTUs. Despite the clear potential for enhancing our understanding with the history of modern-day organisms and their genomes, a vital downside of this `embarrassment of riches’ will be the fact that many phylogenetic trees are produced utilizing datasets that have been trimmed down to a `manageable’ size for methodological and/or presentation purposes [1,2]. A typical adjustment would be to reduce the dataset size to a level examinable by the human eye on a case-by-case basis. A big variety of similarity search hits are usually retrieved iteratively and sorted, with all the user manually retaining sequences from taxa of interest along with some arbitrarily* Correspondence: [email protected] 1 Department of Biochemistry Molecular Biology, Dalhousie University, Halifax, NS, Canada 2 Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, Canada Full list of author information is obtainable in the end of the articlechosen representatives from other `less important’ taxa. Alternatively, all sequences offered with similarity scores above a particular threshold is often aligned and applied to construct a `quick and dirty’ tree, primarily based on which choices are produced about which sequences to keep and which to discard. A second tree within the desired quantity of OTUs is then constructed. Despite the fact that such procedures are commonplace, they are likely to be performed in an ad hoc, subjective fashion that may be difficult to accurately reproduce.1-Bromo-2-chloro-4,5-difluorobenzene Chemscene Here we present TreeTrimmer, a technique for minimizing the complexity and redundancy of phylogenetic trees by removal of phylogenetically and taxonomically closely connected OTUs, with minimal loss of taxonomic diversity.5-(Aminomethyl)picolinic acid Chemscene Two useful applications in the method are discussed herein.PMID:26644518 MethodsPhylogenetic tree constructionFor tree constructions, homologous sequences have been collected employing BLASTP v2.two.26+ (option: -evalue 1e-5 max_target_seqs 2000, unless otherwise specified in figure legends) [3], and aligned with MAFFT v6.864 (choice: –auto –anysymbol) [4]. Right after trimming the several sequence alignments making use of trimAL v1.four (choice: -?2013 Maruyama et al.; licensee BioMed Central Ltd. This is an Open Access report distributed below the terms of your Inventive Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original perform is effectively cited.Maruyama et al. BMC Research Notes 2013, 6:145 http://biomedcentral/1756-0500/6/Page 2 ofgt 0.eight) [5], approximately-maximum-likelihood phylogenetic trees had been constructed with fasttree v2.1.3 (alternative: pseudo -spr 4 -mlacc 2 -slownne -wag -gamma) [6].The `TreeTrimmer’ procedureTreeTrimmer is usually a command-line program written in Ruby, developed.