TY - JOUR AU - Efron, B. PY - 1979 DA - 1979// TI - Bootstrap Methods: Another Look at the Jackknife JO - Annals Stat VL - 7 UR - https://doi.org/10.1214/aos/1176344552 DO - 10.1214/aos/1176344552 ID - Efron1979 ER - TY - JOUR AU - Felsenstein, J. PY - 1985 DA - 1985// TI - Confidence limits on phylogenies: An approach using the bootstrap JO - Evolution VL - 39 UR - https://doi.org/10.2307/2408678 DO - 10.2307/2408678 ID - Felsenstein1985 ER - TY - JOUR AU - Penny, D. AU - Foulds, L. R. AU - Hendy, M. D. PY - 1982 DA - 1982// TI - Testing the theory of evolution by comparing phylogenetic trees constructed from 5 different protein sequences JO - Nature VL - 297 UR - https://doi.org/10.1038/297197a0 DO - 10.1038/297197a0 ID - Penny1982 ER - TY - CHAP AU - Huelsenbeck, J. P. AU - Hillis, D. M. AU - Jones, R. ED - Ferraris, J. D. ED - Palumbi, S. R. PY - 1995 DA - 1995// TI - Parametric bootstrapping in molecular phylogenetics: Applications and performance. Molecular zoology: Advances, Strategies, and Protocols BT - Symposium held during Annual Meeting of the American Society of Zoologists, St. Louis, Missouri, USA, January 5-8 PB - Wiley-Liss Inc CY - New York ID - Huelsenbeck1995 ER - TY - CHAP AU - Swofford, D. L. AU - Olson, G. J. AU - Waddell, P. J. AU - Hillis, D. M. ED - Hillis, D. M. ED - Moritz, C. ED - Mable, B. K. PY - 1996 DA - 1996// TI - Phylogenetic inference BT - Molecular Systematics PB - Sunderland, Massachusetts CY - Sinauer Associates ID - Swofford1996 ER - TY - JOUR AU - Goldman, N. AU - Anderson, J. P. AU - Rodrigo, A. G. PY - 2000 DA - 2000// TI - Likelihood-based tests of topologies in phylogenetics JO - Syst. Biol VL - 49 UR - https://doi.org/10.1080/106351500750049752 DO - 10.1080/106351500750049752 ID - Goldman2000 ER - TY - JOUR AU - Storm, C. E. V. AU - Sonnhammer, E. L. L. PY - 2002 DA - 2002// TI - Automated ortholog inference from phylogenetic trees and calculation of orthology reliability JO - Bioinformatics VL - 18 UR - https://doi.org/10.1093/bioinformatics/18.1.92 DO - 10.1093/bioinformatics/18.1.92 ID - Storm2002 ER - TY - JOUR AU - Burleigh, J. G. AU - Driskell, A. C. AU - Sanderson, M. J. PY - 2006 DA - 2006// TI - Supertree bootstrapping methods for assessing phylogenetic variation among genes in genome-scale data sets JO - Syst. Biol VL - 55 UR - https://doi.org/10.1080/10635150500541722 DO - 10.1080/10635150500541722 ID - Burleigh2006 ER - TY - JOUR AU - Seo, T. K. PY - 2008 DA - 2008// TI - Calculating bootstrap probabilities of phylogeny using multilocus sequence data JO - Mol. Biol. Evol VL - 25 UR - https://doi.org/10.1093/molbev/msn043 DO - 10.1093/molbev/msn043 ID - Seo2008 ER - TY - JOUR AU - Susko, E. PY - 2008 DA - 2008// TI - On the Distributions of Bootstrap Support and Posterior Distributions for a Star Tree JO - Syst. Biol VL - 57 UR - https://doi.org/10.1080/10635150802302468 DO - 10.1080/10635150802302468 ID - Susko2008 ER - TY - JOUR AU - Soltis, P. S. AU - Soltis, D. E. PY - 2003 DA - 2003// TI - Applying the Bootstrap in Phylogeny Reconstruction JO - Statistical Science VL - 18 UR - https://doi.org/10.1214/ss/1063994980 DO - 10.1214/ss/1063994980 ID - Soltis2003 ER - TY - CHAP AU - Linder, C. AU - Warnow, T. ED - Aluru, S. PY - 2005 DA - 2005// TI - An Overview of Phylogeny Reconstruction BT - Handbook of Computational Molecular Biology ID - Linder2005 ER - TY - JOUR AU - Felsenstein, J. PY - 1978 DA - 1978// TI - Cases in which parsimony or compatibility methods will be positively misleading JO - Syst. Zool VL - 27 UR - https://doi.org/10.2307/2412923 DO - 10.2307/2412923 ID - Felsenstein1978 ER - TY - BOOK AU - Felsenstein, J. PY - 2004 DA - 2004// TI - Inferring Phylogenies PB - Sinauer Assoc CY - Sunderland, Massachusetts ID - Felsenstein2004 ER - TY - JOUR AU - Hayasaka, K. AU - Gojobori, T. AU - Horai, S. PY - 1988 DA - 1988// TI - Molecular phylogeny and evolution of primate mitochondrial DNA JO - Mol. Biol. Evol VL - 5 ID - Hayasaka1988 ER - TY - JOUR AU - Woese, C. R. AU - Olsen, G. AU - Ibba, M. AU - Söll, D. PY - 2000 DA - 2000// TI - Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process JO - Microbiol. Mol. Biol. Rev VL - 64 UR - https://doi.org/10.1128/MMBR.64.1.202-236.2000 DO - 10.1128/MMBR.64.1.202-236.2000 ID - Woese2000 ER - TY - JOUR AU - Saitou, N. AU - Nei, N. PY - 1987 DA - 1987// TI - The neighbor-joining method: a new method for reconstructing phylogenetic trees JO - Mol. Biol. Evol VL - 4 ID - Saitou1987 ER - TY - CHAP AU - Jukes, T. H. AU - Cantor, C. PY - 1969 DA - 1969// TI - Mammalian Protein Metabolism BT - Evolution of protein molecules PB - Academic Press CY - New York ID - Jukes1969 ER - TY - BOOK AU - Kimura, M. PY - 1983 DA - 1983// TI - The neutral theory of molecular evolution PB - Cambridge University Press CY - Cambridge UR - https://doi.org/10.1017/CBO9780511623486 DO - 10.1017/CBO9780511623486 ID - Kimura1983 ER - TY - JOUR AU - Hayasaka, K. AU - Fujii, K. AU - Horai, S. PY - 1996 DA - 1996// TI - Molecular phylogeny of macaques: implications of nucleotide sequences from an 896-base pair region of mitochondrial DNA JO - Mol. Biol. Evol VL - 13 UR - https://doi.org/10.1093/oxfordjournals.molbev.a025655 DO - 10.1093/oxfordjournals.molbev.a025655 ID - Hayasaka1996 ER - TY - CHAP AU - Makarenkov, V. AU - Legendre, P. ED - Kiers, H. A. L. ED - Rasson, J. P. ED - Groenen, P. J. F. ED - Schader, M. PY - 2000 DA - 2000// TI - Improving the additive tree representation of a given dissimilarity matrix using reticulations BT - Data analysis, Classification and Related Methods UR - https://doi.org/10.1007/978-3-642-59789-3_5 DO - 10.1007/978-3-642-59789-3_5 ID - Makarenkov2000 ER - TY - JOUR AU - Wildman, D. E. AU - Bergman, T. J. AU - al-Aghbari, A. AU - Sterner, K. N. PY - 2004 DA - 2004// TI - Mitochondrial evidence for the origin of hamadryas baboons JO - Mol. Phyl. Evol VL - 32 UR - https://doi.org/10.1016/j.ympev.2003.12.014 DO - 10.1016/j.ympev.2003.12.014 ID - Wildman2004 ER - TY - JOUR AU - Li, D. AU - Fan, L. AU - Zeng, B. AU - Yin, H. PY - 2009 DA - 2009// TI - The complete mitochondrial genome of Macaca thibetana and a novel nuclear mitochondrial pseudogene JO - Gene VL - 429 UR - https://doi.org/10.1016/j.gene.2008.10.010 DO - 10.1016/j.gene.2008.10.010 ID - Li2009 ER - TY - JOUR AU - Boc, A. AU - Philippe, H. AU - Makarenkov, V. PY - 2010 DA - 2010// TI - Inferring and validating horizontal gene transfer events using bipartition dissimilarity JO - Syst. Biol VL - 59 UR - https://doi.org/10.1093/sysbio/syp103 DO - 10.1093/sysbio/syp103 ID - Boc2010 ER - TY - JOUR AU - Loria, A. AU - Pan, T. PY - 2001 DA - 2001// TI - Modular construction for function of a ribonucleoprotein enzyme: the catalytic domain of Bacillus subtilis RNase P complexed with B.subtilis RNase P protein JO - Nucleic Acids Res VL - 29 UR - https://doi.org/10.1093/nar/29.9.1892 DO - 10.1093/nar/29.9.1892 ID - Loria2001 ER - TY - JOUR AU - Ambrogelly, A. AU - Korencic, D. AU - Ibba, M. PY - 2002 DA - 2002// TI - Functional Annotation of Class I Lysyl-tRNA Synthetase Phylogeny Indicates a Limited Role for Gene Transfer JO - J. Bacteriol VL - 184 UR - https://doi.org/10.1128/JB.184.16.4594-4600.2002 DO - 10.1128/JB.184.16.4594-4600.2002 ID - Ambrogelly2002 ER - TY - JOUR AU - Gogarten, J. P. AU - Doolittle, W. F. AU - Lawrence, J. G. PY - 2002 DA - 2002// TI - Prokaryotic Evolution in Light of Gene Transfer JO - Mol. Biol. Evol VL - 19 UR - https://doi.org/10.1093/oxfordjournals.molbev.a004046 DO - 10.1093/oxfordjournals.molbev.a004046 ID - Gogarten2002 ER - TY - JOUR AU - Novichkov, P. S. AU - Omelchenko, M. V. AU - Gelfand, M. S. AU - Mironov, A. A. AU - Wolf, Y. I. AU - Koonin, E. V. PY - 2004 DA - 2004// TI - Genome-Wide Molecular Clock and Horizontal Gene Transfer in Bacterial Evolution JO - J. Bacteriol VL - 186 UR - https://doi.org/10.1128/JB.186.19.6575-6585.2004 DO - 10.1128/JB.186.19.6575-6585.2004 ID - Novichkov2004 ER - TY - JOUR AU - Roy, H. AU - Ling, J. AU - Alfonzo, J. AU - Ibba, M. PY - 2005 DA - 2005// TI - Loss of Editing Activity during the Evolution of Mitochondrial Phenylalanyl-tRNA Synthetase JO - J. Biol. Chem VL - 280 UR - https://doi.org/10.1074/jbc.M508281200 DO - 10.1074/jbc.M508281200 ID - Roy2005 ER - TY - CHAP AU - Makarenkov, V. AU - Boc, A. AU - Delwiche, C. F. AU - Diallo, A. B. AU - Philippe, H. ED - Batagelj, V. ED - Ferligoj, A. ED - Ziberna, A. PY - 2006 DA - 2006// TI - New efficient algorithm for modeling partial and complete gene transfer scenarios BT - Data Science and Classification UR - https://doi.org/10.1007/3-540-34416-0_37 DO - 10.1007/3-540-34416-0_37 ID - Makarenkov2006 ER - TY - JOUR AU - McAuliffe, L. AU - Ellis, R. J. AU - Miles, K. AU - Ayling, R. D. AU - Nicholas, R. A. J. PY - 2006 DA - 2006// TI - Biofilm formation by mycoplasma species and its role in environmental persistence and survival JO - Microbiology VL - 152 UR - https://doi.org/10.1099/mic.0.28604-0 DO - 10.1099/mic.0.28604-0 ID - McAuliffe2006 ER - TY - JOUR AU - Simader, H. AU - Hothorn, M. AU - Kohler, C. AU - Basquin, J. AU - Simos, G. AU - Suck, D. PY - 2006 DA - 2006// TI - Structural basis of yeast aminoacyl-tRNA synthetase complex formation revealed by crystal structures of two binary sub-complexes JO - Nucleic Acids Res VL - 34 UR - https://doi.org/10.1093/nar/gkl560 DO - 10.1093/nar/gkl560 ID - Simader2006 ER - TY - JOUR AU - Brindefalk, B. AU - Viklund, J. AU - Larsson, D. AU - Thollesson, M. AU - Andersson, S. G. E. PY - 2007 DA - 2007// TI - Origin and Evolution of the Mitochondrial Aminoacyl-tRNA Synthetases JO - Mol. Biol. Evol VL - 24 UR - https://doi.org/10.1093/molbev/msl202 DO - 10.1093/molbev/msl202 ID - Brindefalk2007 ER - TY - JOUR AU - Felsenstein, J. PY - 1989 DA - 1989// TI - PHYLIP - Phylogeny Inference Package (Version 3.2) JO - Cladistics VL - 5 ID - Felsenstein1989 ER - TY - JOUR AU - Hillis, D. M. AU - Bull, J. J. PY - 1993 DA - 1993// TI - An Empirical Test of Bootstrapping as a Method for Assessing Confidence in Phylogenetic Analysis JO - Syst. Biol VL - 42 UR - https://doi.org/10.1093/sysbio/42.2.182 DO - 10.1093/sysbio/42.2.182 ID - Hillis1993 ER - TY - JOUR AU - Felsenstein, J. AU - Kishino, H. PY - 1993 DA - 1993// TI - Is There Something Wrong with the Bootstrap on Phylogenies? A Reply to Hillis and Bull JO - Syst. Biol VL - 42 UR - https://doi.org/10.1093/sysbio/42.2.193 DO - 10.1093/sysbio/42.2.193 ID - Felsenstein1993 ER - TY - JOUR AU - Efron, B. AU - Halloran, E. AU - Holmes, S. PY - 1996 DA - 1996// TI - Bootstrap confidence levels for phylogenetic trees JO - PNAS VL - 93 UR - https://doi.org/10.1073/pnas.93.23.13429 DO - 10.1073/pnas.93.23.13429 ID - Efron1996 ER - TY - JOUR AU - Efron, B. AU - Tibshirani, R. PY - 1998 DA - 1998// TI - The problem of regions JO - Ann. Statist VL - 26 UR - https://doi.org/10.1214/aos/1024691353 DO - 10.1214/aos/1024691353 ID - Efron1998 ER - TY - CHAP AU - Gullo, F. AU - Tagarelli, A. AU - Greco, S. PY - 2009 DA - 2009// TI - Diversity-based Weighting Schemes for Clustering Ensembles BT - 9th SIAM International Conference on Data Mining (SDM '09), Sparks, Nevada, USA, April 30-May 2 ID - Gullo2009 ER - TY - CHAP AU - Fern, X. AU - Brodley, C. ED - Fawcett, T. ED - Mishra, N. PY - 2003 DA - 2003// TI - Random Projections for High Dimensional Data Clustering: A Cluster Ensemble Approach BT - Proc. Int. Conf. on Machine Learning (ICML) PB - AAAI Press, USA CY - Washington, D.C. ID - Fern2003 ER - TY - JOUR AU - Kuncheva, L. I. AU - Hadjitodorov, S. T. PY - 2004 DA - 2004// TI - Using Diversity in Cluster Ensembles JO - Proc. IEEE Int. Conf. on Systems, Man and Cybernetics (SMC), The Hague, The Netherlands VL - 2 ID - Kuncheva2004 ER - TY - CHAP AU - Domeniconi, C. AU - Al-Razgan, M. PY - 2009 DA - 2009// TI - Weighted Cluster Ensembles: Methods and Analysis BT - ACM Trans. on Knowledge Discovery from Data (TKDD) ID - Domeniconi2009 ER - TY - JOUR AU - Lapointe, F. J. AU - Cucumel, G. PY - 1997 DA - 1997// TI - The Average Consensus Procedure: Combination of Weighted Trees Containing Identical or Overlapping Sets of Objects JO - Syst. Biol VL - 46 UR - https://doi.org/10.1093/sysbio/46.2.306 DO - 10.1093/sysbio/46.2.306 ID - Lapointe1997 ER - TY - JOUR AU - Ronquist, F. PY - 1996 DA - 1996// TI - Matrix Representation of Trees, Redundancy, and Weighting JO - Syst. Biol VL - 45 UR - https://doi.org/10.1093/sysbio/45.2.247 DO - 10.1093/sysbio/45.2.247 ID - Ronquist1996 ER -