Přepnout na evidenci publikací, které mě citují.
MACHOLÁN, Miloš. Základy fylogenetické analýzy. 1. vyd. Brno: Masarykova univerzita, 2014. 290 s. ISBN 978-80-210-6363-1. doi:10.5817/CZ.MUNI.M210-6363-2014.
Adachi, J., Hasegawa, M. (1992) MOLPHY: Programs for Molecular Phylogenetics 1 – PROTML: Maximum Likelihood Inference of Protein Phylogeny. Computer Science Monographs, No. 27. Institute of Statistical Mathematics, Tokyo.
Adachi, J., Hasegawa, M. (1996). Model of amino acid substitution in proteins encoded by mitochondrial DNA. Journal of Molecular Evolution 42: 459–468.
DOI: 10.1007/BF02498640
Adachi, J., Waddell, P.J., Martin, W., Hasegawa, M. (2000). Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA. Journal of Molecular Evolution 50: 348–358.
Akaike, H. (1974) A new look at the statistical model identification. IEEE Transactions on Automatic Control 19: 716–723.
DOI: 10.1109/TAC.1974.1100705
Albert, V. (ed.) (2006). Parsimony, Phylogeny, and Genomics. Oxford University Press, Oxford.
Albrecht, B., Scornavacca, C., Cenci, A., Huson, D.H. (2012). Fast computation of minimum hybridization networks. Bioinformatics 28: 191–197.
DOI: 10.1093/bioinformatics/btr618
Archie, J. W. (1985). Methods for coding variable morphological features for numerical taxonomic analysis. Systematic Zoology 34: 326–345.
DOI: 10.2307/2413151
Archie, J. W. (1989). A randomization test for phylogenetic information in systematic data. Systematic Zoology 38: 239–252.
DOI: 10.2307/2992285
Aris-Brosou, S., Yang, Z. (2002). Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan 18S ribosomal RNA phylogeny. Systematic Biology 51: 703–714.
DOI: 10.1080/10635150290102375
Avise, J. C. (2000). Phylogeography: The History and Formation of Species. Harvard University Press, Cambridge, MA.
Avise, J. C., Robinson, T.J. (2008). Hemiplasy: A new term in the lexicon of phylogenetics. Systematic Biology 57: 503–507.
DOI: 10.1080/10635150802164587
Balding, D. J., Bishop, M., Cannings, C. (eds.) (2007). Handbook of Statistical Genetics, 3rd edition. John Wiley & Sons, Chichester.
Barry, D., Hartigan, J.A. (1987). Statistical analysis of hominoid molecular evolution. Statistical Science 2: 191–210.
DOI: 10.1214/ss/1177013353
Baum, B. R. (1992). Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees. Taxon 41: 3–10.
DOI: 10.2307/1222480
Bininda-Emonds, O. R. P. (2004). The evolution of supertrees. Trends in Ecology and Evolution 19: 315–322.
DOI: 10.1016/j.tree.2004.03.015
Bishop, M. J., Friday, A.E. (1987). Tetrapod relationships: the molecular evidence. In Patterson, C. (ed.): Molecules and morphology in evolution: conflict or compromise? Cambridge University Press, Cambridge, England, pp. 123–139.
Bookstein, F. L. (1994). Can biometrical shape be a homologous character? In Hall, B.K. (ed.): Homology: The Hierarchical Basis of Comparative Biology. Academic Press, New York, pp. 197–227.
Bookstein, F. L. (2000). Creases as local features of deformation grids. Medical Image Analysis 4: 93–110.
DOI: 10.1016/S1361-8415(00)00015-3
Bookstein, F. L. (2002). Creases as morphometric characters. In MacLeod, N., Forey, P.L. (eds.): Morphology, Shape and Phylogenetics. Taylor & Francis, London, pp. 139–174.
Bourque, M. (1978). Arbres de Steiner et reseaux dont certains sommets sont ( localisation variable. Unpublished Ph.D. thesis. Université de Montréal.
Bremer, K. (1988). The limits of amino-acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42: 795–803.
DOI: 10.2307/2408870
Bremer, K. (1990). Combinable component consensus. Cladistics 6: 369–372.
DOI: 10.1111/j.1096-0031.1990.tb00551.x
Bryant, D. (2003). A classification of consensus methods for phylogenetics. In Janowitz, M. F., Lapointe, F.-J., McMorris, F. R., Mirkin, B., Roberts, F. S. (eds.): Bioconsensus. DIMACS Series in Discrete Mathematics and Theoretical Computer Science, Vol. 61. American Mathematical Society, Providence, RI, pp. 163–184.
Buerki, S., Forest, F., Salamin, N., Alvarez, N. (2011). Comparative performance of supertree algorithms in large data sets using the soapberry family (Sapindaceae) as a case study. Systematic Biology 60: 32–44.
DOI: 10.1093/sysbio/syq057
Butler, M. A., King, A.A. (2004). Phylogenetic comparative analysis: A modeling approach for adaptive evolution. American Naturalist 164: 683–695.
DOI: 10.1086/426002
Cao, Y., Janke, A., Waddell, P.J., Westerman, M., Takenaka, O., Murata, S., Okada, N., Pääbo, S., Hasegawa, M. (1998). Conflict amongst individual mitochondrial proteins in resolving the phylogeny of eutherian orders. Journal of Molecular Evolution 47: 307–322.
DOI: 10.1007/PL00006389
Cavalli-Sforza, L.L., Edwards, A.W.F. (1967). Phylogenetic analysis: Models and estimation procedures. Evolution 32: 550–570.
DOI: 10.2307/2406616
Cavender, J.A., Felsenstein, J. (1987). Invariants of phylogenies in a simple case with discrete states. Journal of Classification 4: 57–71.
DOI: 10.1007/BF01890075
Criscuolo, A., Berry, V., Douzery, E.J., Gascuel, O. (2006). SDM: A fast distance-based approach for (super)tree building in phylogenomics. Systematic Biology 55: 740–755.
DOI: 10.1080/10635150600969872
Dayhoff, M.O. (1972). Atlas of Protein Sequence and Structure. National Biomedical Research Foundation, Silver Springs, MD.
Dayhoff, M.O., Eck, R.V. (1968). Atlas of Protein Sequence and Structure 1967–1968. National Biomedical Research Foundation, Silver Spring, MD.
Dayhoff, M.O., Schwartz, R.M., Orcutt, B.C. (1978). A model of evolutionary change in proteins. In Dayhoff, M.O. (ed.): Atlas of Protein Sequence and Structure, vol. 5, suppl. 3. National Biomedical Research Foundation, Silver Springs, MD, pp. 345–352.
De Queiroz, A. (1993). For consensus (sometimes). Systematic Biology 42: 368–372.
DOI: 10.1093/sysbio/42.3.368
Dimmic, M.W., Rest, J.S., Mindell, D.P., Goldstein, D. (2002). RArtREV: An amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny. Journal of Molecular Evolution 55: 65–73.
DOI: 10.1007/s00239-001-2304-y
Doolittle, R.F., Blombäck, B. (1964). Amino-acid sequence investigations of fibrinopeptides from various mammals: Evolutionary implications. Nature 202: 147–52.
DOI: 10.1038/202147a0
Drummond, A.J., Ho, S.Y., Phillips, M.J., Rambaud, A. (2006). Relaxed phylogenetics and dating with confidence. PLoS Biology 4: e88.
DOI: 10.1371/journal.pbio.0040088
Drummond, A.J., Rambaut, A. (2007). BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology 7: 214.
DOI: 10.1186/1471-2148-7-214
Drummond, A.J., Rambaut, A., Shapiro, B., Pybus, O.G. (2005). Bayesian coalescent inference of past population dynamics from molecular sequences. Molecular Biology and Evolution 22:1185–1192.
Eck, R.V., Dayhoff, M.O. (eds.) (1966). Atlas of Protein Sequence and Structure. National Biomedical Research Foundation, Silver Springs, MD.
Edwards, A.W.F. (1970) Estimation of the branch points of a branching diffusion process. Journal of the Royal Statistical Society B 32: 155–174.
Edwards, A.W.F., Cavalli-Sforza, L.L. (1963). The reconstruction of evolution. Annals of Human Genetics 18: 105–106.
Efron, B., Halloran, E., Holmes, S. (1996). Bootstrap confidence levels for phylogenetic trees. Proceedings of the National Academy of Science, USA 93: 13429–13434.
DOI: 10.1073/pnas.93.23.13429
Estabrook, G.F., McMorris, F.R., Meacham, C.A. (1985). Comparison of undirected phylogenetic trees based on subtrees of 4 evolutionary units. Systematic Zoology 34: 193–200.
DOI: 10.2307/2413326
Faith, D.P., Cranston, P.S. (1991). Could a cladogram this sort have arisen by chance alone? On permutation tests for cladistic structure. Cladistics 7: 1–28.
DOI: 10.1111/j.1096-0031.1991.tb00020.x
Faith, D.P. (1991). Cladistic permutation tests for monophyly. Systematic Zoology 40: 366–375.
DOI: 10.2307/2992329
Farris, J.S. (1970). Methods for computing Wagner trees. Systematic Zoology 34: 21–34.
Farris, J.S. (1976). Expected asymmetry of phylogenetic trees. Systematic Zoology 25: 196–198.
DOI: 10.2307/2412748
Farris, J.S. (1977). Phylogenetic analysis under Dollo’s Law. Systematic Zoology 26: 77–88.
DOI: 10.2307/2412867
Farris, J.S. (1989). The retention index and the rescaled consistency index. Cladistics 5: 417–419.
DOI: 10.1111/j.1096-0031.1989.tb00573.x
Farris, J.S., Källersjö, M., Kluge, A.G., Bult, C. (1994). Testing significance of incongruence. Cladistics 10: 315–319.
DOI: 10.1111/j.1096-0031.1994.tb00181.x
Felsenstein, J. (1973a) Maximum likelihood and minimum–steps methods for estimating evolutionary trees from data on discrete characters. Syst. Zool. 22: 240–249.
DOI: 10.2307/2412304
Felsenstein, J. (1973b) Maximum–likelihood estimation of evolutionary trees from continuous characters. American Journal of Human Genetics 25: 471–492.
Felsenstein, J. (1978a) Cases in which parsimony and compatibility methods will be positively misleading. Systematic Zoology 27: 401–410.
DOI: 10.2307/2412923
Felsenstein, J. (1978b). The number of evolutionary trees. Systematic Zoology 27: 27–33.
DOI: 10.2307/2412810
Felsenstein, J. (1981). Evolutionary trees from DNA sequences: A maximum likelihood approach. Journal of Molecular Evolution 17:368–376.
Felsenstein, J. (1984). Distance methods for inferring phylogenies: A justification. Evolution 38: 16–24.
DOI: 10.2307/2408542
Felsenstein, J. (1985a). Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39: 783–791.
DOI: 10.2307/2408678
Felsenstein, J. (1985b). Phylogenies and the comparative method. The The American Naturalist 125: 1–15.
DOI: 10.1086/284325
Felsenstein, J. (2004). Inferring Phylogenies. Sinauer Associates, Sunderland, MA.
Felsenstein, J. (2009). PHYLIP 3.69. Phylogeny Inference Package.
Felsenstein, J., Churchill, G.A. (1996). A hidden Markov model approach to variation among sites in rate of evolution. Molecular Biology and Evolution 13: 93–104.
DOI: 10.1093/oxfordjournals.molbev.a025575
Fisher, R.A. (1912). On an absolute criterion for fitting frequency curves. Messenger of Mathematics 41: 155–160.
Fisher, R.A. (1921). On the “probable” error of a coefficient of correlation deduced from a small sample. Metron 1: 3–32.
Fitch, W.M. (1971). Toward defining the course of evolution: Minimal change for a specific tree topology. Systematic Zoology 20: 406–416.
DOI: 10.2307/2412116
Fitch, W.M., Margoliash, E. (1967). Construction of phylogenetic trees. Science 155: 279–284.
DOI: 10.1126/science.155.3760.279
Gascuel, O. (1997). BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data. Molecular Biology and Evolution 14: 685–695.
DOI: 10.1093/oxfordjournals.molbev.a025808
Gascuel, O. (ed.) (2007). Mathematics of Evolution and Phylogeny. Oxford University Press, Oxford.
Gascuel, O., Steel, M. (eds.) (2003). Reconstructing Evolution: New Mathematical and Computational Advances. Oxford University Press, Oxford.
Gillespie, J.H. (1991). The Causes of Molecular Evolution. Oxford Univesity Press, Oxford.
Giribet, G. (2007). Efficient tree searches with available algorithms. Evolutionary Bioinformatics Online 3: 341–356.
Gittleman, J.L., Kot, M. (1990). Adaptation: statistics and a null model for estimating phylogenetic effects. Systematic Zoology 39: 227–241.
Goldman, N., Yang, Z. (1994). A codon–based model of nucleotide substitution for protein–coding DNA sequences. Molecular Biology and Evolution 11: 725–736.
Goloboff, P.A. (1999). Analyzing large data sets in reasonable times: solutions for composite optima. Cladistics 15: 415–428.
DOI: 10.1111/j.1096-0031.1999.tb00278.x
Goloboff, P.A. (2002). Techniques for analyzing large data sets. In DeSalle, R., Giribet, G., Wheeler, W. (ed.): Techniques in Molecular Systematics and Evolution. Brikhäuser Verlag; Basel, pp. 70–79.
Goodman, M. (1981). Decoding the pattern of protein evolution. Progress in Biophysics and Molecular Biology 37: 105–164.
Gowri-Shankar, V., Rattray, M. (2007). A reversible jump method for Bayesian phylogenetic inference with a nonhomogeneous substitution model. Molecular Biology and Evolution 24: 1286–1299.
DOI: 10.1093/molbev/msm046
Grafen, A. (1989). The phylogenetic regression. Philosophical Transactions of the Royal Society of London, Series B 326: 119–157.
DOI: 10.1098/rstb.1989.0106
Graur, D., Martin, W. (2004). Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision. Trends in Genetics 20: 80–86.
DOI: 10.1016/j.tig.2003.12.003
Green, P.J. (1995). Reversible jump Markov Chain Monte Carlo computation and Bayesian model determination. Biometrika 82: 711–732.
DOI: 10.1093/biomet/82.4.711
Hall, B.G. (2001). Phylogenetic Trees Made Easy: A How-To Manual for Molecular Biologists. Sinauer Associates, Sunderland, MA.
Han, K.-L., Braun, E.L., Kimball, R.T., Reddy, S., Bowie, R.K., Braun, M.J., Chojnowski, J.L., Hackett, S.J., Harshman, J., Huddleston, C.J., Marks, B.D., Miglia, K.J., Moore, W.S., Sheldon, F.H., Steadman, D.W., Witt, C.C., Yuri, T. (2011). Are transposable element insertions homoplasy free?: An examination using the avian Tree of Life. Systematic Biology 60: 375–386.
DOI: 10.1093/sysbio/syq100
Harpending, R.C. (1994). Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Human Biology 66: 591–600.
Hartl, D.L., Clark, A.G. (1997). Principles of Population Genetics, 3rd ed. Sinauer Associates, Sunderland, MA.
Harvey, P.H., Leigh Brown A.J., Maynard Smith, J., Nee, S. (eds.) (1996). New Uses for New Phylogenies. Oxford University Press, Oxford./
Harvey, P.H., Pagel, M.D. (eds.) (1993). The Comparative Method in Evolutionay Biology. Oxford University Press, New York.
Hasegawa, M., Kishino, H., Yano, T. (1985). Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution 22: 160–174.
DOI: 10.1007/BF02101694
Hasegawa, M., Kishino, H., Yano, T. (1987). Man’s place in Hominoidea as inferred from molecular clocks of DNA. Journal of Molecular Evolution 26: 132–147.
DOI: 10.1007/BF02111287
Hasegawa, M., Kishino, H., Yano, T. (1989). Estimation of branching dates among primates by molecular clocks of nuclear DNA which slowed down in Hominoidea. Journal of Human Evolution 18: 461–476.
DOI: 10.1016/0047-2484(89)90075-4
Hastings, W.K. (1970). Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57: 97–109.
DOI: 10.1093/biomet/57.1.97
Heath, T.A. (2012). A hierarchical Bayesian model for calibrating estimates of species divergence times. Systematic Biology 61: 793–809.
DOI: 10.1093/sysbio/sys032
Hedges, S.B. (1992). The number of replications needed for accurate estimation of the bootstrap P value in phylogenetic studies. Molecular Biology and Evolution 9: 366–369.
Hedges, S.B., Kumar, S. (2004). Precision of molecular time estimates. Trends in Genetics 20: 242–247.
Hendy, M.D. (1991). A combinatorial description of the closest tree algorithm for finding evolutionary trees. Discrete Mathematics 91: 51–58.
DOI: 10.1016/0012-365X(91)90469-I
Hendy, M.D., Penny, D. (1982). Branch and bound algorithms to determine minimal evolutionary trees. Mathematical Biosciences 60: 133–142.
Hendy, M.D., Penny, D. (1989). A framework for the quantitative study of evolutionary trees. Systematic Zoology 38: 297–309.
DOI: 10.2307/2992396
Hendy, M.D., Penny, D. (1993) Spectral analysis of phylogenetic data. Journal of Classification 10: 5–24.
DOI: 10.1007/BF02638451
Henikoff, S., Henikoff, J.G. (1992). Amino acid substitution matrices from protein blocks. Proceedings of the Academy of Sciences, USA 89: 10915–10919.
DOI: 10.1073/pnas.89.22.10915
Hennig, W. (1966). Phylogenetic Systematics. University of Illinois Press, Urbana.
Hillis, D.M. (1984). Misuse and modification of Nei’s genetic distance. Systematic Zoology 33: 238–240.
DOI: 10.2307/2413023
Hillis, D.M. (1991). Discriminating between phylogenetic signal and random noise in DNA sequences. In Miyamoto, M.M., Cracraft, J. (eds.): Phylogenetic Analysis of DNA Sequences. Oxford University Press, Oxford, pp. 278–294.
Hillis, D.M., Bull, J.J. (1993). An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Systematic Biology 42: 182–192. Hillis, D.M., Moritz, C., Mable, B.K. (eds.): Molecular Systematics, 2nd ed. Sinauer Associates, Sunderland, MA.
Hillis, D. M., Wiens, J. J. (2000). Molecules versus morphology in systematics: Conflicts, artifacts, and misconceptions. In Wiens, J.J. (eds.): Phylogenetic Analysis of Morphological Data. Smithsonian Institution Press, Washington, DC, pp. 1–19.
Hixson, J., Brown, W.M. (1986). A comparison of the small ribosomal RNA gene from the mitochondrial DNA of the great apes and humans: sequence, structure, evolution, and phylogenetic implications. Molecular Biology and Evolution 3: 1–18.
Ho, S.Y.W., Phillips, M.J. (2009). Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. Systematic Biology 58: 367–380.
DOI: 10.1093/sysbio/syp035
Hudson, R.R. (1991). Gene genealogies and the coalescent process. In Futuyma, D., Antonovics, J. (eds.): Oxford Surveys in Evolutionary Biology, Vol. 7. Oxford University Press, Oxford, pp. 1–44.
Huelsenbeck, J.P. (1995). Performance of phylogenetic methods in simulation. Systematic Biology 44: 17–48.
DOI: 10.1093/sysbio/44.1.17
Huelsenbeck, J.P., Bollback, J.P. (2007). Application of the likelihood function in phylogenetic analysis. In Balding, D.J., Bishop, M., Cannings, C, (eds.): Handbook of Statistical Genetics, 3rd edition. John Wiley & Sons, Chichester, pp. 460–488.
Huelsenbeck, J.P., Bull, J.J., Cunningham, C.W. (1996). Combining data in phylogenetic analysis. Trends in Ecology and Evolution 11: 152–158.
Huelsenbeck, J.P., Hillis, D.M. (1993). Success of phylogenetic methods in the four–taxon case. Systematic Biology 42: 247–264.
DOI: 10.1093/sysbio/42.3.247
Huelsenbeck, J.P., Larget, B., Alfaro, M.E. (2004) Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo. Molecular Biology and Evolution 21: 1123–1133.
DOI: 10.1093/molbev/msh123
Huelsenbeck, J.P., Larget, B., Swofford, D. (2000a). A compound Poisson process for relaxing the molecular clock. Genetics 154: 1879–1892.
Huelsenbeck, J.P., Ronquist, F., Hall, B. (2000b). MrBayes: A Program for the Bayesian Inference of Phylogeny. [http://morphbank.ebc.uu.se/mrbayes/]
Huson, D.H., Scornavacca, C. (2012). Dendroscope 3: An interactive tool for rooted phylogenetic trees and networks. Systematic Biology 61: 1061–1067.
DOI: 10.1093/sysbio/sys062
Chen, D., Diao, L., Eulenstein, O., Fernandez-Baca, D., Sanderson, M. (2003). Flipping: A supertree construction method. In Janowitz, M.F., Lapointe, F.-J., McMorris, F.R., Mirkin, B., Roberts, F.S. (eds.): Bioconsensus. DIMACS Series in Discrete Mathematics and Theoretical Computer Science, Vol. 61. American Mathematical Society, Providence, RI, pp. 135–160.
Chen, Z.-Z., Wang, L. (2010). HybridNet: A tool for constructing hybridization networks. Bioinformatics 26: 2912–2913.
DOI: 10.1093/bioinformatics/btq548
Chen, Z.-Z., Wang, L., Yamanaka, S. (2012). A fast tool for minimum hybridization networks. BMC Bioinformatics 13: 155.
DOI: 10.1186/1471-2105-13-155
Cheverud, J.M., Dow, M.M., Leutengger, W. (1985). The quantitative assessment of phylogenetic constraints in comparative analyses: Sexual dimorphism in body weight among primates. Evolution 39: 1335–1351.
DOI: 10.2307/2408790
Churchill, G.A., von Haeseler, A., Navidi, W.C. (1992). Sample size for a phylogenetic inference. Molecular Biology and Evolution 9: 753–769.
Jones, D.T., Taylor, W.R., Thornton, J.M. (1992) The rapid generation of mutation data matrices from protein sequences. Computer Applied Bioscience 8: 25–282.
Jukes, T.H., Cantor, C.R. (1969). Evolution of protein molecules. In Munro, H.N. (ed.): Mammalian Protein Metabolism. Academic Press, New York, pp. 21–132.
Kim, J.H., Antunes, A., Luo, S.J., Menninger, J., Nash, W.G., O’Brien, S.J. (2006). Evolutionary analysis of a large mtDNA translocation (numt) into the nuclear genome of the Panthera genus species. Gene 366: 292–302.
DOI: 10.1016/j.gene.2005.08.023
Kimura, M. (1968). Evolutionary rate at the molecular level. Nature 217: 624–626.
DOI: 10.1038/217624a0
Kimura, M. (1969). The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations. Genetics 61: 893–903.
Kimura, M. (1980). A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16: 111–120.
DOI: 10.1007/BF01731581
Kimura, M. (1981). Estimation of evolutionary distances between homologous nucleotide sequences. Proceedings of the National Academy of Sciences, USA 78: 454–458.
DOI: 10.1073/pnas.78.1.454
Kimura, M. (1983). The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge.
Kimura, M., Crow, J. (1964). The number of alleles that can be maintained in a finite population. Genetics 49: 725–738.
Kimura, M., Ohta, T. (1972). On the stochastic model for estimation of mutational distance between homologous proteins. Journal of Molecular Evolution 2: 87–90.
DOI: 10.1007/BF01653945
King, J.L., Jukes, T.H. (1969). Non-Darwinian evolution. Science 164: 788–798.
DOI: 10.1126/science.164.3881.788
Kingman, J.F.C. (1982). The coalescent. Stochastic Processes and Their Applications 13: 235–248.
Kishino, H., Hasegawa, M. (1989) Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. Journal of Molecular Evolution 29: 170–179.
DOI: 10.1007/BF02100115
Kishino, H., Miyata, T., Hasegawa, M. (1990) Maximum likelihood inference of protein phylogeny and the origin of chloroplasts. Journal of Molecular Evolution 31:151–160.
Kitching, I.J., Forey, P.L., Humphries, C.J., Williams, D.M. (eds.) (1993). Cladistics: A Practical Course in Systematics. Oxford University Press, Oxford.
Kitching, I.J., Forey, P.L., Humphries, C.J., Williams, D.M. (1998). Cladistics: The Theory and Practice of Parsimony Analysis. The Systematics Association Publication No. 11, Oxford University Press, Oxford.
Klingenberg, C.P., Gidaszewski, N.A. (2010). Testing and quantifying phylogenetic signals and homoplasy in morphometric data. Systematic Biology 59: 245–261.
DOI: 10.1093/sysbio/syp106
Kluge, A.G. (1998). Total evidence or taxonomic incongruence: Cladistics or consensus classification. Cladistics 14: 151–158.
DOI: 10.1111/j.1096-0031.1998.tb00328.x
Kluge, A., Farris, J. (1969) Quantitative phyletics and the evolution of anurans. Systematic Zoology 18: 1–32.
DOI: 10.2307/2412407
Knowles, L.L., Kubatko, L.S. (eds.) (2010). Estimating Species Trees: Practical and Theoretical Aspects. Wiley-Blackwell.
Kuhner, M.K., Felsenstein, J. (1994). A simulation comparison of phylogeny algorithms under equal and unequal evolutiobnary rates. Molecular Biology and Evolution 11: 459–468 (Erratum 12: 525, 1995).
Kuhner, M.K., Yamato, J., Felsenstein, J. (1995). Estimating effective populations size and mutation rate from sequence data using Metropolis-Hastings sampling. Genetics 140: 1421–1430.
Kuhner, M.K., Yamato, J., Felsenstein, J. (1998). Maximum likelihood estimation of population gerowth rates based on the coalescent. Genetics 149: 429–434.
Kumar, S. (1996). A stewise algorithm for finding minimum evolutionary trees. Molecular Biology and Evolution 13: 584–593.
DOI: 10.1093/oxfordjournals.molbev.a025618
Kuo,L., Chen, M.-H., Lewis, P.O. (eds.) (2014). Bayesian Phylogenetics: Methods, Computational Algorithms, and Applications. CRC Press.
Lake, J.A. (1994). Reconstructing evolutionary trees from DNA and protein sequences: Paralinear distances. Proceeding of the National Academy of Sciences, USA 91: 1455–1459.
DOI: 10.1073/pnas.91.4.1455
Lanyon, S. (1985). Detecting internal inconsistencies in distance data. Systematic Zoology 34: 397–403.
DOI: 10.2307/2413204
Lemey, P., Salemi, M., Vandamme, A.-M. (eds.) (2009). The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny. Cambridge University Press, Cambridge.
Lapointe, J.F., Cucumel, G. (1997). The average consensus procedure: combination of weighted trees containing identical or overlapping sets of taxa. Systematic Biology 46: 306–312.
DOI: 10.1093/sysbio/46.2.306
Li, S. (1996). Phylogenetic Tree Construction Using Markov Chain Monte Carlo. Ph.D. dissertation, Ohio State University, Columbus.
Li, W.-H., Graur, D. (1991). Molecular Evolution. Sinauer Associates, Sunderland, MA.
Lockhart, P.J., Steel, M.A., Hendy, M.D., Penny, D. (1994). Recovering evolutionary trees under a more realistic model of sequence evolution. Molecular Biology and Evolution 11: 605–612.
Macholán M. (2008). The mouse skull as a source of morphometric data for phylogeny inference. Zoologischer Anzeiger 247: 315–327.
Macholán M. (2006). A geometric morphometric analysis of the shape of the first upper molar in mice of the genus Mus (Muridae, Rodentia). Journal of Zoology 270: 672–681.
MacLeod, N., Forey, P.L. (eds.) (2002). Morphology, Shape and Phylogeny. Taylor & Francis, London, New York.
Maddison, W.P. (1990). A method for testing the correlated evolution of two binary characters: Are gains and losses concentrated on certain branches of a phylogenetic tree? Evolution 44: 539–557.
Marcus, L.F., Corti, M., Loy, A., Naylor, G.J.P., Slice, D.E. (eds.) (1996). Advances in Morphometrics. Plenusm Press, New York, London.
Margoliash, E. (1963). Primary structure and evolution of cytochrome c. Proceedings of the National Academy of Sciences, USA 50: 672–679.
DOI: 10.1073/pnas.50.4.672
Margush, T. McMorris, F.R. (1981). Consensus n-trees. Bulletin of Mathematical Biology 43: 239–244.
Marhold, K., Suda, J. (2002). Statistické zpracování mnohorozměrných dat v taxonomii (Fenetické metody). Karolinum, Praha.
Martins, E.P. (1994). Estimating the rate of phenotypic evolution from comparative data. The American Naturalist 144: 193–209.
DOI: 10.1086/285670
Martins, E.P. (ed.) (1996). Phylogenies and the Comparative Method in Animal Behaviour. Oxford University Press, New York.
Martins, E.P., Hansen, T.F. (1996). The statistical analysis of interspecific data: a review and evaluation of phylogenetic comparative methods. In Martins, M. (ed.): Phylogenies and the Comparative Method in Animal Behavior. Oxford University Press, Oxford.
Mau, B. (1996). Bayesian Phylogenetic Inference Via Markov Chain Monte Carlo Methods. Ph.D. dissertation, University of Wisconsin, Madison.
Metropolis, N., Rosenbluth, A.W., Rosenbluth, M.N., Teller, A.H., Teller, E. (1953). Equations of state calculations by fast computing machines. Journal of Chemical Physics 21: 1087–1091.
DOI: 10.1063/1.1699114
Mitteroecker, P., Gunz, P. (2009). Advances in geometric morphometrics. Evolutionary Biology 36: 235–247.
DOI: 10.1007/s11692-009-9055-x
Miyamoto, M.M., Fitch, W.M. (1995). Testing species phylogenies and phylogenetic methods with congruence. Systematic Biology 44: 64–76.
DOI: 10.1093/sysbio/44.1.64
Monteiro, L.R. (2000). Why morphometrics is special: the problem with using partial warps as characters for phylogenetic inference. Systematic Biology 49: 796–800.
DOI: 10.1080/106351500750049833
Moore, G.W. (1976) Proof for the maximum parsimony (“Red King”) algorithm. In Goodman, M., Tashian, R.E. (eds.): Molecular Anthropology. Plenum Press, New York, pp. 117–137.
Mueller, L.D., Ayala, F.J. (1982). Estimation and interpretation of genetic distance in empirical studies. Genetical Research 40: 127–137.
DOI: 10.1017/S0016672300019005
Müller, T., Vingron, M. (2000). Modeling amino acid replacement. Journal of Computational Biology 7: 761–776.
DOI: 10.1089/10665270050514918
Muse, S.V. (1995). Evolutionary analyses of DNA sequences subject to constraints on secondary structure. Genetics 139: 1429–1439.
Muse, S.V., Gaut, B.S. (1994). A likelihood approach for comparing synonymous and nonsynonymous substitution rates, with application to the chloroplast genome. Molecular Biology and Evolution 11: 715–724.
Muse, S.V., Kosakovsky Pond, S.I. (2000). HYPHY: Hypothesis Testing Using Phylogenies. (North Carolina State University, Raleigh), Version 1.
Nei, M. (1972). Genetic distance between populations. The American Naturalist106: 283–292.
Nei, M. (1978). Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89: 583–590.
Nei, M., Kumar, S. (2000). Molecular Evolution and Phylogenetics. Oxford University Press, Oxford.
Nei, M., Li, W.-H. (1979). Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences, USA 76: 5269–5273.
DOI: 10.1073/pnas.76.10.5269
Nelson, G. (1979). Cladistic analysis and synthesis: Principles and definitions, with a historical note on Adanson’s Familles des Plantes (1763–1764). Systematic Zoology 28: 1–21.
Neyman, J. (1971). Molecular studies of evolution: A source of novel statistical problems. In Gupta, S.S., Yackel, J. (eds.): Statistical Decision Theory and Related Topics. Academic Press, New York, pp. 1–27.
Nixon, K.C. (1999). The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics 15: 407–414.
DOI: 10.1111/j.1096-0031.1999.tb00277.x
Nixon, K.C., Carpenter, J.M. (1996). On simultaneous analysis. Cladistics 12: 221–241.
DOI: 10.1111/j.1096-0031.1996.tb00010.x
Nordborg, M. (2007). Coalescent theory. In Balding, D.J., Bishop, M., Cannings, C, (eds.): Handbook of Statistical Genetics, 3rd edition. John Wiley & Sons, Chichester, pp. 843–877.
Novacek, M.J., Wheeler, Q. D. (1992). Extinct taxa—accounting for 99.9990 . . .% of the earth’s biota. In Novacek, M.J., Wheeler, Q. D. (eds.): Extinction and Phylogeny. Columbia University Press, New York, 1–16.
Ohno, S. (1970). Evolution by Gene Duplication. Springer-Verlag.
O’Meara, B.C., Ane, C., Sanderson, M.J., Wainwright, P.C. (2006). Testing for different rates of continuous trait evolution using likelihood. Evolution 60: 922–933.
DOI: 10.1111/j.0014-3820.2006.tb01171.x
Pääbo, S. (1998). Genomes, Mutations And Phylogenies. Springer-Verlag, Berlin.
Page, R.D.M. (1990). Component analysis: A valiant failure? Cladistics 6: 119–136.
DOI: 10.1111/j.1096-0031.1990.tb00532.x
Page, R.D.M. (ed.) (2002). Tangled Trees: Phylogeny, Cospeciation, and Coevolution. University of Chicago Press, Chicago, IL.
Page, R.D.M., Holmes, E.C. (1998). Molecular Evolution. A Phylogenetic Approach. Blackwell Science, Oxford.
Pagel, M. (1994). Detecting correlated evolution on phylogenies: A general method for the comparative analysis of discrete characters. Proceedings of the Royal Society of London, Series B 255: 37–45.
DOI: 10.1098/rspb.1994.0006
Pagel, M., Meade, A. (2004) A phylogenetic mixture model for detecting pattern–heterogeneity in gene sequence or character-state data. Systematic Biology 53: 571–581.
DOI: 10.1080/10635150490468675
Pattengale, N.P., Alipour, M., Bininda-Emonds, O.R.P., Moret, B.M.E., Stamatakis, A. (2010). How many bootstrap replicates are necessary? Journal of Computational Biology 17: 337–354.
DOI: 10.1089/cmb.2009.0179
Penny, D., Lockhart, P.J., Steel, M.A., Hendy, M.D. (1994). The role of models in reconstructing evolutionary trees. In Scotland, R.W., Siebert, D.J., Williams, D.M. (eds.): Models in Phylogeny Reconstructions. Systematic Association Special Volume No. 52. Clarendon Press, Oxford.
Penny, D., Hendy, M.D., Lockhart, P.J., Steel, M.A. (1996). Corrected parsimony, minimum evolution, and Hadamrd conjugations. Systematic Biology 45: 596–606.
DOI: 10.1093/sysbio/45.4.596
Poe, S., Wiens, J.J. (2000). Character selection and the methodology of morphological phylogenetics. In Wiens, J.J. (eds.): Phylogenetic Analysis of Morphological Data. Smithsonian Institution Press, Washington, DC, 20–36.
Posada, D. (2003). Selecting models of evolution. In In Salemi, M., Vandamme, A.-M. (eds.): The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny. Cambridge University Press, Cambridge, pp. 256–282.
Posada, D., Buckley, T.R. (2004) Model selection and model averaging in phylogenetics: advantages of Akaike Information Criterion and Bayesian approaches over Likelihood Ratio Tests. Systematic Biology 53: 793–808.
DOI: 10.1080/10635150490522304
Prager, E.M., Wilson, A.C. (1988). Ancient origin of lactalbumin from lysozyme: Analysis of DNA and amino acid sequences. Journal of Molecular Evolution 27: 326–335.
DOI: 10.1007/BF02101195
Ragan, M.A. (1992). Phylogenetic inference based on matrix representation of trees. Molecular Phylogenetics and Evolution 1: 53–58.
DOI: 10.1016/1055-7903(92)90035-F
Rambaut, A., Bromham, L. (1998). Estimating divergence dates from molecular sequences. Molecular Biology and Evolution 15: 442–448.
DOI: 10.1093/oxfordjournals.molbev.a025940
Rannala, B., Yang, Z. (1996) Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. Journal of Molecular Evolution 43: 304–311.
DOI: 10.1007/BF02338839
Reeves, J.H. (1992). Heterogeneity in the substitution process of amino acid sites of proteins coded for by mitochondrial DNA. Journal of Molecular Evolution 35: 17–31.
DOI: 10.1007/BF00160257
Robinson, D.F., Foulds, L.R. (1979). Comparison of weighted labelled trees. In Horadam, A.F., Wallis, W.D. (eds.): Combinatorial Mathematics VI. Proceedings of the Sixth Australian Conference of Combinatorial Mathematics, Armidale, Australia. Lecture Notes in Mathematics, No. 748. Springer-Verlag, Berlin.
Robinson, D.F., Foulds, L.R. (1981). Comparison of phylogenetic trees. Mathematical Biosciences 53: 131–147.
Rogers, A.R., Harpending, H. (1992). Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution 9: 552–569.
Rogers, J.S. (1972). Measures of genetic similarity and genetic distance. Studies in Genetics. VII. University of Texas Publications 7213: 1912–1919.
Rohlf, F.J. (1982). Consensus indices for comparing classifications. Mathematical Biosciences 59: 131–144.
DOI: 10.1016/0025-5564(82)90112-2
Rohlf, F.J. (1998). On applications of geometric morpohometrics to studies of ontogeny and phylogeny. Systematic Biology 47: 147–158.
DOI: 10.1080/106351598261094
Rohlf, F.J. (2001). Comparative methods for the analysis of continuous variables: Geometric interpretations. Evolution 55: 243–260.
DOI: 10.1111/j.0014-3820.2001.tb00731.x
Rohlf, F.J. (2004). Geometric morphometrics in systematics. In MacLeod, N., Forey, P.L. (eds.): Morphology, Shape and Phylogenetics. Taylor & Francis, London, pp. 175–193.
Rohlf, F.J., Marcus, L.F. (1993). A revolution in morphometrics. Trends in Ecology and Evolution 8:129–132.
Ronquist, F., Huelsenbeck, J.P. (2003). MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572–1574.
DOI: 10.1093/bioinformatics/btg180
Ronquist, F., Huelsenbeck, J.P., van der Mark, P. (2005). MrBayes 3.1. Manual. Draft 5/26/2005.
Rzhetsky, A., Nei, M. (1992). A simple method for estimating and testing minimum-evolution trees. Molecular Biology and Evolution 9: 945–967.
Rzhetsky, A., Nei, M. (1993). Theoretical foundations of the minimum-evolution method of phylogenetic inference. Molecular Biology and Evolution 10: 1073–1095.
Saitou, N. (1991). Statistical methods for phylogenetic tree reconstruction. In Rao, C.R., Chakraborty, R. (eds.): Handbook of Statistics, Vol. 8, Applications in Biology and Medicine. Elsevier cience Publishers, pp. 317–346.
Saitou, N., Nei, M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4: 406–425. Salemi, M., Vandamme, A.-M. (eds.): The Phylogenetic Handbook. A Practical Approach to DNA and Protein Phylogeny. Cambridge University Press, Cambridge
Sanderson, M.J. (2002). Estimating absolute rates of molecular evolution and divergence times: A penalized likelihood approach. Molecular Biology and Evolution 19: 101–109.
DOI: 10.1093/oxfordjournals.molbev.a003974
Sang, T. (1995). New measurements of distribution of homoplasy and reliability of parsimonious cladograms. Taxon 44: 77–82.
DOI: 10.2307/1222680
Sankoff, D. (1975). Minimal mutation trees of sequences. SIAM Journal of Applied Mathematics 28: 35–42.
DOI: 10.1137/0128004
Sankoff, D.D., Rousseau, P. (1975). Locating the vertices of a Steiner tree in arbitrary space. Mathematical Programming 9: 240–246.
DOI: 10.1007/BF01681346
Sarich, V.M., Wilson, A.C. (1973). Generation time and genomic evolution in primates. Science 179: 1144–1147.
DOI: 10.1126/science.179.4078.1144
Scotland, R.W., Siebert, D., Williams, D.M. (eds.) (1994). Models in Phylogeny Reconstruction. Oxford University Press, Oxford.
Scornavacca, C., Berry, V., Lefort, V., Douzery, E.J.P, Ranwez, V. (2008). PhySIC_IST: cleaning source trees to infer more informative supertrees. BMC Bioinformatics 9: 413.
DOI: 10.1186/1471-2105-9-413
Semple, C., Steel, M. (2003). Phylogenetics. Oxford University Press, Oxford.
Seo, T.-K. (2008). Calculating bootstrap probabilities of phylogeny using multilocus sequence data. Molecular Biology and Evolution 25: 960–971.
Seo, T.-K., Kishino, H., Thorne J.L. (2005). Incorporating gene-specific variation when inferring and evaluating optimal evolutionary tree topologies from multilocus sequence data. Proceedings of the National Academy of Sciences, USA 102: 4436–4441.
Shimodaira, H. (2002). An approximately unbiased test of phylogenetic tree selection. Systematic Biology 51:492–508.
Shimodaira, H., Hasegawa, M. (1999). Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution 16: 1114–1116.
DOI: 10.1093/oxfordjournals.molbev.a026201
Schöniger,M., von Haeseler, A. (1994). A stochastic model for the evolution of autocorrelated DNA sequences. Molecular Phylogenetics and Evolution 3: 240–247.
DOI: 10.1006/mpev.1994.1026
Schwarz, G. (1978) Estimating the dimension of a model. Annals of Statistics 6: 461–464.
DOI: 10.1214/aos/1176344136
Siddall, M.E. (1998). Success of parsimony in the four-taxon case: long-branch repulsion by likelihood in the Farris zone. Cladistics 14: 209–220.
DOI: 10.1111/j.1096-0031.1998.tb00334.x
Sievers, F., Wilm, A., Dineen, D., Gibson, T.J., Karplus, K., Li, W., Lopez, R., McWilliam, H., Remmert, M., Söding, J., Thompson, J.D., Higgins, D.G. (2011). Fast, scalable generation of high quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology 7: 539.
DOI: 10.1038/msb.2011.75
Slatkin, M., Hudson, R.R. (1991). Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129: 555–562.
Slowinski, J.B., Guyer, C. (1989). Testing the stochasticity of patterns of organismal diversity: An improved null model. The American Naturalist 134: 907–921.
DOI: 10.1086/285021
Soltis, D.E., Soltis, P.S. (2003). Applying the bootstrap in phylogeny reconstruction. Statistical Science 18: 256–267.
DOI: 10.1214/ss/1063994980
Soltis, P.S., Soltis, D.E., Chase, M.W. (1999). Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology. Nature 402: 402–404.
Stamatakis, A. (2006). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 21: 2688–2690.
DOI: 10.1093/bioinformatics/btl446
Stamatakis, A., Hoover, P., Rougemont, J. (2008). A rapid bootstrap algorithm for the RAxML web servers. Systematic Biology 57: 758–771.
DOI: 10.1080/10635150802429642
Steel, M.A. (1989) Distribution of Bicolored Evolutionary Trees. Ph.D. Thesis, Massey Univ., Palmerston North, New Zealand.
Steel, M.A., Hendy, M.D., Penny, D. (1993). Parsimony can be consistent. Systematic Zoology 42: 581–587.
Strait, D., Moritz, M., Strait, P. (1996). Finite mixture coding: A new approach to coding continuous characters. Systematic Biology 45: 67–78.
DOI: 10.1093/sysbio/45.1.67
Strimmer, K., von Haeseler, A. (1996). Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies. Molecular Biology and Evolution13: 964–969.
Strimmer, K., von Haeseler, A. (2003). Nucleotide substitution models: Theory. In Salemi, M., Vandamme, A.-M. (eds.): The Phylogenetic Handbook. A Practical Approach to DNA and Protein Phylogeny. Cambridge University Press, Cambridge, pp. 72–87.
Suchard, M.A., Weiss, R.E., Dorman, K.S., Sinsheimer, J.S. (2003). Inferring spatial phylogenetic variation along nucleotide sequences: a multiple changepoint model. Journal of the American Statistical Association 98: 427–437.
DOI: 10.1198/016214503000215
Svoboda, J.A. (2014). Předkové. Evoluce člověka. Academia Praha.
Swenson, M.S., Suri, R., Linder, C.R., Warnow, T. (2012). SuperFine: Fast and accurate supertree estimation. Systematic Biology 61: 214–227.
DOI: 10.1093/sysbio/syr092
Swofford, D.L., Berlocher, S.H. (1987). Inferring evolutionary trees from gene frequency data under the principle of maximum parsimony. Systematic Zoology 36: 293–325.
DOI: 10.2307/2413068
Swofford, D.L., Maddison, W.P. (1987). Reconstructing ancestral character states under Wagner parsimony. Mathematical Biosciences 87: 199–229.
DOI: 10.1016/0025-5564(87)90074-5
Swofford, D.L., Olsen, G.J., Waddell, P.J., Hillis, D.M. (1996). Phylogenetic inferrence. In Hillis, D.M., Moritz, C., Mable, B.K. (eds.): Molecular Systematics, 2nd ed. Sinauer Associates, Sunderland, MA, pp. 407–514.
Swofford, D.L., Sullivan, J. (2003). Phylogeny inference based on parsimony and other methods using PAUP*. In Salemi, M., Vandamme, A.-M. (eds.): The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny. Cambridge University Press, Cambridge, pp. 160–206.
Swofford, D.L., Waddell, P.J., Huelsenbeck, J.P., Foster, P.G., Lewis, P.O., Rogers, J.S. (2001). Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Systematic Biology 50: 525–539.
DOI: 10.1080/106351501750435086
Tajima, F., Nei, M. (1982) Biases of the estimates of DNA divergence obtained by the restriction enzyme technique. Journal of Molecular Evolution 17: 115–120.
DOI: 10.1007/BF01810830
Takezaki, N., Rzhetsky, A., Nei, M. (1995). Phylogenetic test of the molecular clock and linearized trees. Molecular Biology and Evolution 12: 823–833.
Tamura, K. (1992). The rate and pattern of nucleotide substitution in Drosophila mitochondrial DNA. Molecular Biology and Evolution 9: 814–825.
Tamura, K., Nei, M. (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution 10: 512–526.
Tarver, J.E., Sperling, E.A., Nailor, A., Heimberg, A.M., Robinson, J.M., King, B.L., Pisani, D., Donoghue, P.C.J., Peterson, J.J. (2013). miRNAs: Small genes with big potential in metazoan phylogenetics. Molecular Biology and Evolution, doi:10.1093/molbev/mst133.
DOI: 10.1093/molbev/mst133
Tavaré, S. (1986). Some probabilistic and statisical problems on the analysis of DNA sequences. Lectures on Mathematics in the Life Sciences 17: 57–86.
Templeton, A.R. (1983). Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and apes. Evolution 37: 221–244.
DOI: 10.2307/2408332
Thiele, K. (1993). The holy grail of the perfect character: The cladistic treatment of morphometric data. Cladistics 9: 275–304.
DOI: 10.1111/j.1096-0031.1993.tb00226.x
Thiele, K., Ladiges, P.Y. (1988). A cladistic analysis of Angophora Cav. (Myrtaceae). Cladistics 4: 23–42.
DOI: 10.1111/j.1096-0031.1988.tb00466.x
Thompson, J.D., Higgins, D.G., Gibson, T.J. (1994). Clustal W – improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22: 4673–4680.
DOI: 10.1093/nar/22.22.4673
Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F. and Higgins, D.G. (1997). The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 25: 4876–4882.
DOI: 10.1093/nar/25.24.4876
Thorne, J.L., Kishino, H., Painter, I.S. (1998). Estimating the rate of evolution of the rate of molecular evolution. Molecular Biology and Evolution 15: 1647–1657.
DOI: 10.1093/oxfordjournals.molbev.a025892
Tillier, E.R.M., Collins, R.A. (1995) Neighbor joining and maximum likelihood with RNA sequences: addressing the interdependence of sites. Molecular Biology and Evolution 12: 7–15.
DOI: 10.1093/oxfordjournals.molbev.a040195
Waddell, P.J., Penny, D. (1996) Extending Hadamard conjugations to model sequence evolution with variable rates across sites. [Přístupné prostřednictvím anonymního ftp ze serveru onyx.si.edu.]
Whelan, S., Goldman, N. (2001). A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Molecular Biology and Evolution 18: 691–699.
DOI: 10.1093/oxfordjournals.molbev.a003851
White, W.T.J., Holland, B.R. (2011). Faster exact maximum parsimony search with XMP. Bioinformatics 27: 1359–1367.
DOI: 10.1093/bioinformatics/btr147
Wiens, J.J. (1998a). Combining data sets with different phylogenetic histories. Systematic Biology 47: 568–581.
DOI: 10.1080/106351598260581
Wiens, J.J. (1998b). Does adding characters with missing data increase or decrease phylogenetic accuracy? Systematic Biology 47: 625–640.
DOI: 10.1080/106351598260635
Wiens, J.J. (1998c). Testing phylogenetic methods with tree-congruence: Phylogenetic analysis of polymorphic morphological characters in phrynostomatid lizards. Systematic Biology 47: 411–428.
DOI: 10.1080/106351598260806
Wiens, J.J. (1998d). The accuracy of methods for coding and sampling higher-level taxa for phylogenetic analysis: A simulation study. Systematic Biology 47: 381–397.
DOI: 10.1080/106351598260789
Wiens, J.J. (ed.) (2000). Phylogenetic Analysis of Morphological Data. Smithsonian Institution Press, Washington, London.
Wiens, J.J. (2003). Incomplete taxa, incomlpete characters, and phylogenetic accuracy: Is there a missing data problem? Journal of Vertebrate Paleontology 23: 297–310.
DOI: 10.1671/0272-4634(2003)023[0297:ITICAP]2.0.CO;2
Wiens, J.J., Morrill, M.C. (2011). Missing data in phylogenetic analysis: Reconciling results from simulations and empirical data. Systematic Biology 60: DOI:10.1093/sysbio/syr025
DOI: 10.1093/sysbio/syr025
Wiens, J.J., Servedio, M.R. (1997). Accuracy of phylogenetic analysis including and excluding polymorphic characters. Systematic Biology 46: 332–345.
DOI: 10.1093/sysbio/46.2.332
Wiley, E.O. (1981). Phylogenetics: The Theory and Practice of Phylogenetic Systematics. John Wiley, New York.
Wiley, E.O., Siegel-Causey, D., Brooks, D.R., Funk, V.A. (1991). The Compleat Cladist. A Primer of Phylogenetic Procedures. The University of Kansas, Museum of Natural History Special Publications No. 19. Lawrence, Kansas, KS.
Wolfe, K. (2000). Robustness – it’s not where you think it is. Nature Genetics 25: 3–4.
Wu, C.-H., Suchard, M.A., Drummond, AJ. (2013). Bayesian selection of nucleotide substitution models and their site assignments. Molecular Biology and Evolution 30: 669–688.
DOI: 10.1093/molbev/mss258
Wu, Y. (2013). An algorithm for constructing parsimonious hybridization networks with multiple phylogenetic trees. In: Deng, M., Jiang, R., Sun, F., Zhang, X. (eds.) Research in Computational Molecular Biology. Pp. 291–303. Spriger-Verlag, Berlin, Heidelberg.
Xia, X. (2007). Bioinformatics and the cell: modern computational approaches in genomics, proteomics and transcriptomics. Springer-Verlag, Berlin.
Yang, Z. (1994) Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods. Journal of Molecular Evolution 39: 306–314.
DOI: 10.1007/BF00160154
Yang, Z. (1997) PAML: A program package for phylogenetic analysis by maximum likelihood. CABIOS 13: 555–556.
Yang, Z., Nielsen, R., Hasegawa, M. (1998). Models of amino acid substitution and applications to mitochondrial protein evolution. Molecular Biology and Evolution 15: 1600–1611.
DOI: 10.1093/oxfordjournals.molbev.a025888
Yoder, A.D., Yang, Z.H. (2000). Estimation of primate speciation dates using local molecular clocks. Molecular Biology and Evolution 17: 1081–1090.
DOI: 10.1093/oxfordjournals.molbev.a026389
Zelditch, M.L., Fink, W.L., Swiderski, D.L. (1995). Morphometrics, homology, and phylogenetics: Quantitative characters as synapomorphies. Systematic Biology 44: 179–189.
DOI: 10.1093/sysbio/44.2.179
Zelditch, M.L., Swiderski, D.L., Sheets, D.H., Fink, W.L. (2004). Geometric Morphometrics for Biologists: A Primer. Elsevier, Oxford.
Zharkikh, A. (1994). Estimation of evolutionary distances between nucleotide sequences. Journal of Molecular Evolution 39: 315–329.
DOI: 10.1007/BF00160155
Zharkikh, A., Li, W.-H. (1993). Inconsistency of the maximum-parsimony method: The case of five taxa with a molecular clock. Systematic Biology 42: 113–125.
DOI: 10.1093/sysbio/42.2.113
Zharkikh, A., Li, W.-H. (1995). Estimation of confidence in phylogeny: The complete-and-partial bootstrap technique. Molecular Phylogenetics and Evolution 4: 44–63.
DOI: 10.1006/mpev.1995.1005
Zima, J., Macholán, M., Munclinger, P., Piálek, J. (2004). Genetické metody v zoologii. Karolinum Praha.
Zuckerkandl, E., Pauling, L. (1962). Molecular disease, evolution, and genetic heterogeneity. In Kasha, M., Pullman, B. (eds.): Horizons in Biochemistry. Academic Press, New York, pp. 189–225.