Oinformatics, Dalhousie University, Halifax, NS, Canada. 3Integrated Microbial Biodiversity Plan, Canadian Institute for Advanced Investigation, Montreal, QC H3A 1A4, Canada. 4McGill University and G ome Qu ec, 740 Docteur-Penfield Ave, Montreal, QC H3A 1A4, Canada. Received: 24 December 2012 Accepted: eight April 2013 Published: 12 April 2013 References 1. Krishnamoorthy M, Patel P, Dimitrijevic M, Dietrich J, Green M, Macken C: Tree pruner: an effective tool for choosing information from a biased genetic database. BMC Bioinforma 2011, 12:51. 2. Zaslavsky L, Tatusova T: Mining the NCBI influenza sequence database: adaptive grouping of BLAST final results working with precalculated neighbor indexing. PLoS Curr 2009, 1, RRN1124. three. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215:403?ten. 4. Katoh K, Asimenos G, Toh H: Several alignment of DNA sequences with MAFFT. Approaches Mol Biol 2009, 537:39?four.Conclusions Current advances in genome and transcriptome sequencing have enabled taxon-rich sampling for single or a number of gene phylogenetic analyses. Nevertheless, it’s not trivial to make sure balanced taxon sampling in an objective and reproducible way. We created a tree-based dereplication system for pruning redundant OTUs from phylogenetic datasets determined by assistance values, branch lengths and taxonomic information linked to each sequence. This method enables the user to reproducibly obtain lowered OTU datasets with user-defined parameters, yielding alignments amenable for use having a wider array of computer-intensive downstream analyses in automated or manual phylogenetic pipelines. Availability and requirements TreeTrimmer script and sample information are out there at the following Google Code site (http://code.google/p/ treetrimmer/). More fileAdditional file 1: Figure S1. Phylogeny of Cytochrome c oxidase subunit two proteins. A) Phylogenetic tree of Cytochrome c oxidase subunit two proteins utilised in Figure 1A, with complete descriptions of organismal names and accession numbers.2,3-Dichloro-5-fluoropyridine uses Parameter input files (B) and (C) had been utilised to generate the trees shown in Figure 1B and C, respectively, with each other with the Newick format input tree file (D) as well as the reference list of OTU names and taxonomic facts (E).1210830-60-6 In stock Figure S2.PMID:23671446 PsbO protein phylogeny using the query from Arabidopsis thaliana making use of various settings. Settings wereMaruyama et al. BMC Study Notes 2013, six:145 http://biomedcentral/1756-0500/6/Page 5 of5.Capella-Guti rez S, Silla-Mart ez JM, Gabald T: trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 2009, 25:1972?973. 6. Cost MN, Dehal PS, Arkin AP: FastTree 2 pproximately maximumlikelihood trees for large alignments. PLoS 1 2010, 5:e9490. 7. Curtis BA, Tanifuji G, Burki F, Gruber A, Irimia M, Maruyama S, Arias MC, Ball SG, Gile GH, Hirakawa Y, Hopkins JF, Kuo A, Rensing SA, Schmutz J, Symeonidi A, Elias M, Eveleigh RJM, Herman EK, Klute MJ, Nakayama T, Obornik M, Reyes-Prieto A, Armbrust EV, Aves SJ, Beiko RG, Coutinho P, Dacks JB, Durnford DG, Fast NM, Green BR, Grisdale CJ, Hempel F, Henrissat B, H pner MP, Ishida K-I, Kim E, Koen?L, Kroth PG, Liu Y, Malik S-B, Maier U-G, McRose D, Mock T, Neilson JAD, Onodera NT, Poole AM, Pritham EJ, Richards TA, Rocap G, Roy SW, Sarai C, Schaack S, Shirato S, Slamovits CH, Spencer DF, Suzuki S, Worden AZ, Zauner S, Barry K, Bell C, Bharti AK, Crow JA, Grimwood J, Kramer R, Lindquist E, Lucas S, Salamov A, McFadden GI, Lane CE.