DendroUPGMA: A dendrogram construction utility. Created at March 2002.       By Dr. Santi Garcia-Vallvé (santi.garcia-vallve AT urv.net) and Dr. Pere PuigboBiochemistry and Biotechnology Department.Universitat Rovira i Virgili (URV). Tarragona. Spain.

 Use this program to create a dendrogram from (a) a set of variables, (b) a similarity matrix or (c) a distance matrix. The program calculates a similarity matrix (only for option a), transforms similarity coefficients into distances and makes a clustering using the Unweighted Pair Group Method with Arithmetic mean (UPGMA) algorithm. For Option (a) -Construct a dendrogram from a set of variables- two input formats are available: Format 1: fasta-like format - Two lines,the first one must begin with the ">" character (this will be the identifier line) and the secon one that contains the variables (separated by tabs or spaces, not a combination of both). Format 2: Only one line for each set of variables (separated by spaces). The first one will be assumed to be the identifier. For Options (b) and (c) -Construct a dendrogram from a similarity or distance matrix- the input must be a similarity or distance matrix in CSV or tab-delimited format.

 Choose the input: (a) a set of variables Choose the coefficient used to compare between set of variables: Pearson (r)  Jaccard (Tanimoto)   Dice  MSD   RMSD If the Pearson coefficient (r) has been choosed, choose the transformation of r to generate the distance values (d): d = (1 - r) * 100     d = - Ln (abs (r)) Do you want to generate 100 bootstrap replicates? No Yes Do you want to omit rows with identical values for all the variables? No Yes (b) a similarity matrix Do you want to omit rows with a similarity of 1? No Yes (c) a distance matrix

 This method of dendrogram construction has been used in the following articles: S. Garcia-Vallve, J. Palau and A. Romeu (1999) Horizontal gene transfer in glycosyl hydrolases inferred from codon usage in Escherichia coli and Bacillus subtilis. Molecular Biology and Evololution 16(9):1125-1134. S. Garcia-Vallve, A. Romeu and J. Palau (2000) Horizontal gene transfer of glycosyl hydrolases of the rumen fungi. Molecular Biology and Evolution 17(3):352-361. Garcia-Vallve S, Simo FX, Montero MA, Arola L, Romeu A (2002) Simultaneous horizontal gene transfer of a gene coding for ribosomal protein l27 and operational genes in Arthrobacter sp. J Mol Evol 55:632-637 Reguant C, Bordons A. (2003) Typification of Oenococcus oeni strains by multiplex RAPD-PCR and study of population dynamics during malolactic fermentation. J Appl Microbiol.95:344-353 Bravo IG, Garcia-Vallve S, Romeu A, Reglero A (2004) Prokaryotic origin of cytidylyltransferases and alfa-ketoacid synthases.Trends Microbiol 12:120-128. Gaudier E, Michel C, Segain JP, Cherbut C and Hoebler C (2005) The VSL# 3 probiotic mixture modifies microflora but does not heal chronic dextran-sodium sulfate-induced colitis or reinforce the mucus barrier in mice. J Nutr. 135:2753-2761. Loncaric I, Oberlerchner JT, Heissenberger B, Moosbeckhofer R. (2009) Phenotypic and genotypic diversity among strains of Aureobasidium pullulans in comparison with related species. Antonie Van Leeuwenhoek 95(2):165-178 I. Loncaric, H. Heigl, E. Licek, R. Moosbeckhofer, H-J. Busse and R. Rosengarten (2009) Typing of Pantoea agglomerans isolated from colonies of honey bees (Apis mellifera) and culturability of selected strains from honey. Apidologie 40:40-54 Takumi S, Nishioka E, Morihiro H, Kawahara T, Matsuoka Y. (2009) Natural variation of morphological traits in wild wheat progenitor Aegilops tauschii Coss. BREEDING SCIENCE 59(5):579-588 Lane, D.J.W., Rowe, F.W.E. (2009) A new species of Asterodiscides (Echinodermata, Asteroidea, Asterodiscididae) from the tropical southwest Pacific, and the biogeography of the genus revisited. Zoosystema 31(3):419-429 Brunings, AM; Moyer, C; Peres, N; Folta, KM (2010) Implementation of simple sequence repeat markers to genotype Florida strawberry varieties. EUPHYTICA 173(1):63-75 Csoma, H; Zakany, N; Capece, A; Romano, P; Sipiczki, M (2010) Biological diversity of Saccharomyces yeasts of spontaneously fermenting wines in four wine regions: Comparative genotypic and phenotypic analysis. INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY 140 (2-3): 239-248 Liu, Z; Blasch, E; Xue, Z;, Zhao, J; Laganiére, R; Wu, W (2012) Objective assessment of multiresolution image fusion algorithms for context enhancement in Night vision: A comparative study. IEEE Transactions on Pattern Analysis and Machine Intelligence 34: 94-109 Okpodu, C.M., Khan, G.F., Abdullah-Israel, M. (2012) Characterization of genetic similarity of a Hampton Road (Virginia) Live Oak (Quercus virginiana Mil. L.) to a historic Q. virginiana using rapd markers. Journal of Plant Sciences 7(4):154-162 Yu, J.Z., Fang, D.D., Kohel, R.J., Ulloa, M., Hinze, L.L., Percy, R.G., Zhang, J., Chee, P., Scheffler, B.E., Jones, D.C. (2012) Development of a core set of SSR markers for the characterization of Gossypium germplasm. Euphytica 187(2):203-213 Castillo-Vera, J., Ribas-Aparicio, R.M., Nicolau, C.J., Oliver, A., Osorio-Carranza, L., Aparicio-Ozores, G. (2012) Unusual Diversity of Acquired β-lactamases in Multidrug-Resistant Pseudomonas aeruginosa Isolates in a Mexican Hospital. Microbial Drug Resistance 18(5):471-478 Craig Everroad, R., Otaki, H., Matsuura, K., Haruta, S. (2012) Diversification of bacterial community composition along a temperature gradient at a thermal spring. Microbes and Environments 27(4):374-381 Wullschleger, S., Lacroix, C., Bonfoh, B., Sissoko-Thiam, A., Hugenschmidt, S., Romanens, E., Baumgartner, S., Traoré, I., Yaffee, M., Jans, C., Meile, L. (2013) Analysis of lactic acid bacteria communities and their seasonal variations in a spontaneously fermented dairy product (Malian fènè) by applying a cultivation/genotype-based binary model. International Dairy Journal 29(1):28-35 Bergman, I.-M., Sandholm, K., N. Ekdahl, K., Okumura, N., Uenishi, H., Guldbrandtsen, B., Essler, S.E., Knoll, A., Heegaard, P.M.H., Edfors, I., Juul-Madsen, H.R. (2013) MBL1 genotypes in wild boar populations from Sweden, Austria, the Czech Republic, and Japan. International Journal of Immunogenetics 40(2):131-139 R. L. Hjortshøj, A. R. Ravnshøj, M. Nyman, J. Orabi, G. Backes, H. Pinnschmidt, N. Havis, J. Stougaard, E. H. Stukenbrock (2013) High levels of genetic and genotypic diversity in field populations of the barley pathogen Ramularia collo-cygni. European Journal of Plant Pathology 136(1):51-60 El Kichaoui, A., Abu Zayed, M.A., Ayesh, B.M. (2013) Genotyping and identification of six date palm (Phoenix dactylifera L.) cultivars of the Gaza Strip by random amplification of polymorphic DNA. Emirates Journal of Food and Agriculture 25(11):916-925 Schmidt, M.A., Kreinberg, A.J., Gonzalez, J.M., Halvorson, J.J., French, E., Bollmann, A., Hagerman, A.E. (2013) Soil microbial communities respond differently to three chemically defined polyphenols. Plant Physiology and Biochemistry 72:190-197  If you use this server please mention its URL address and the Garcia-Vallve et al. 1999 article.

DendroUPGMA is included as external resource at the Phylogeny/evolution category from EXPASY Tools