Ic diversity even though retaining the original tree topology, thereby speeding up downstream computer-intensive analyses, e.g., Bayesian and maximum likelihood tree reconstructions, in a reproducible fashion. Keywords: TreeTrimmer, Phylogenetic tree, Pruning, Dereplication, Taxonomic categoryBackground Molecular phylogeny is a strong tool for inferring evolutionary relationships. With advances in high-throughput genome and transcriptome sequencing it is now possible to construct trees from nucleic acid and protein sequence alignments containing a large number of OTUs. Despite the clear potential for improving our understanding from the history of modern-day organisms and their genomes, a crucial downside of this `embarrassment of riches’ will be the truth that quite a few phylogenetic trees are made working with datasets that have been trimmed down to a `manageable’ size for methodological and/or presentation purposes [1,2]. A popular adjustment should be to decrease the dataset size to a level examinable by the human eye on a case-by-case basis.Bucillamine A big variety of similarity search hits are usually retrieved iteratively and sorted, with the user manually retaining sequences from taxa of interest as well as a few 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 data is readily available in the finish of the articlechosen representatives from other `less important’ taxa. Alternatively, all sequences readily available with similarity scores above a particular threshold can be aligned and used to construct a `quick and dirty’ tree, primarily based on which decisions are made about which sequences to maintain and which to discard. A second tree inside the desired number of OTUs is then constructed. While such procedures are commonplace, they are likely to be performed in an ad hoc, subjective fashion that is certainly hard to accurately reproduce. Here we present TreeTrimmer, a system for lowering the complexity and redundancy of phylogenetic trees by removal of phylogenetically and taxonomically closely associated OTUs, with minimal loss of taxonomic diversity. Two useful applications of the strategy are discussed herein.MethodsPhylogenetic tree constructionFor tree constructions, homologous sequences were collected applying BLASTP v2.two.26+ (alternative: -evalue 1e-5 max_target_seqs 2000, unless otherwise specified in figure legends) [3], and aligned with MAFFT v6.864 (choice: –auto –anysymbol) [4]. After trimming the a number of sequence alignments working with trimAL v1.four (alternative: -2013 Maruyama et al.; licensee BioMed Central Ltd. This is an Open Access article distributed below the terms in the Inventive Commons Attribution License (http://creativecommons.Vadastuximab org/licenses/by/2.PMID:24293312 0), which permits unrestricted use, distribution, and reproduction in any medium, offered the original work is appropriately cited.Maruyama et al. BMC Analysis Notes 2013, 6:145 http://www.biomedcentral/1756-0500/6/Page 2 ofgt 0.eight) [5], approximately-maximum-likelihood phylogenetic trees have been constructed with fasttree v2.1.three (choice: pseudo -spr 4 -mlacc two -slownne -wag -gamma) [6].The `TreeTrimmer’ procedureTreeTrimmer is really a command-line system written in Ruby, developed as part of a phylogenomic pipeline applied within the evaluation of algal nuclear genome sequences [7]. As input the plan calls for (i) a Newick formatted tree file with or with out statis.