TY - BOOK AU - Felsenstein, J. PY - 2004 DA - 2004// TI - Inferring Phylogenies PB - Sinauer Associates, Inc CY - Sunderland, Massachusetts ID - Felsenstein2004 ER - TY - JOUR AU - Maddison, W. P. AU - Donoghue, M. J. AU - Maddison, D. R. PY - 1984 DA - 1984// TI - Outgroup analysis and parsimony JO - Syst Zool VL - 33 UR - https://doi.org/10.2307/2413134 DO - 10.2307/2413134 ID - Maddison1984 ER - TY - JOUR AU - Wheeler, W. C. PY - 1990 DA - 1990// TI - Nucleic acid sequence phylogeny and random outgroups JO - Cladistics VL - 6 UR - https://doi.org/10.1111/j.1096-0031.1990.tb00550.x DO - 10.1111/j.1096-0031.1990.tb00550.x ID - Wheeler1990 ER - TY - JOUR AU - Huelsenbeck, J. P. AU - Bollback, J. P. AU - M, L. A. PY - 2002 DA - 2002// TI - Inferring the root of a phylogenetic tree JO - Sys Biol VL - 51 UR - https://doi.org/10.1080/106351502753475862 DO - 10.1080/106351502753475862 ID - Huelsenbeck2002 ER - TY - JOUR AU - Yang, Z. PY - 1994 DA - 1994// TI - Estimating the pattern of nucleotide substitution JO - J Mol Evol VL - 39 ID - Yang1994 ER - TY - JOUR AU - Yang, Z. AU - Roberts, D. PY - 1995 DA - 1995// TI - On the use of nucleic acid sequences to infer early branchings in the tree of life JO - Mol Biol Evol VL - 12 ID - Yang1995 ER - TY - JOUR AU - Galtier, N. AU - Gouy, M. PY - 1998 DA - 1998// TI - Inferring pattern and process: Maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis JO - Mol Biol Evol VL - 15 UR - https://doi.org/10.1093/oxfordjournals.molbev.a025991 DO - 10.1093/oxfordjournals.molbev.a025991 ID - Galtier1998 ER - TY - JOUR AU - Yang, Z. PY - 1996 DA - 1996// TI - Maximum-likelihood models for combined analyses of multiple sequence data JO - J Mol Evol VL - 42 UR - https://doi.org/10.1007/BF02352289 DO - 10.1007/BF02352289 ID - Yang1996 ER - TY - JOUR AU - Brown, W. M. AU - Prager, E. M. AU - Wang, A. AU - Wilson, A. C. PY - 1982 DA - 1982// TI - Mitochondrial DNA sequences of primates, tempo and mode of evolution JO - J Mol Evol VL - 18 UR - https://doi.org/10.1007/BF01734101 DO - 10.1007/BF01734101 ID - Brown1982 ER - TY - JOUR AU - Goldman, N. PY - 1993 DA - 1993// TI - Statistical tests of models of DNA substitution JO - J Mol Evol VL - 36 UR - https://doi.org/10.1007/BF00166252 DO - 10.1007/BF00166252 ID - Goldman1993 ER - TY - JOUR AU - Yang, Z. AU - Goldman, N. AU - Friday, A. PY - 1995 DA - 1995// TI - Maximum likelihood trees from DNA sequences: A peculiar statistical estimation problem JO - Syst Biol VL - 44 UR - https://doi.org/10.1093/sysbio/44.3.384 DO - 10.1093/sysbio/44.3.384 ID - Yang1995 ER - TY - JOUR AU - Yang, Z. PY - 1993 DA - 1993// TI - Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites JO - Mol Biol Evol VL - 10 ID - Yang1993 ER - TY - JOUR AU - Barry, D. AU - Hartigan, J. A. PY - 1987 DA - 1987// TI - Statitstical analysis of hominoid molecular evolution JO - Statistical Science VL - 2 UR - https://doi.org/10.1214/ss/1177013353 DO - 10.1214/ss/1177013353 ID - Barry1987 ER - TY - JOUR AU - Chang, J. T. PY - 1996 DA - 1996// TI - Full reconstruction of Markov models on evolutionary trees: Identiflability and consistency JO - Mathematical Biosciences VL - 137 UR - https://doi.org/10.1016/S0025-5564(96)00075-2 DO - 10.1016/S0025-5564(96)00075-2 ID - Chang1996 ER - TY - JOUR AU - Felsenstein, J. PY - 1981 DA - 1981// TI - Evolutionary trees from DNA sequences: a maximum likelihood approach JO - J Mol Evol VL - 17 UR - https://doi.org/10.1007/BF01734359 DO - 10.1007/BF01734359 ID - Felsenstein1981 ER - TY - JOUR AU - Lanave, C. AU - Preparata, G. AU - Saccone, C. AU - Serio, G. PY - 1984 DA - 1984// TI - A new method for calculating evolutionary substitution rates JO - J Mol Evol VL - 20 UR - https://doi.org/10.1007/BF02101990 DO - 10.1007/BF02101990 ID - Lanave1984 ER - TY - JOUR AU - Tavaré, S. PY - 1986 DA - 1986// TI - Some probabilistic and statistical probles in the analysis of DNA sequences JO - Lectures on Mathematics in the Life Sciences VL - 17 ID - Tavaré1986 ER - TY - CHAP AU - Jukes, T. H. AU - Cantor, C. ED - Munro, H. N. PY - 1969 DA - 1969// TI - Evolution of protein molecules BT - In Mammalian Protein Metabolism UR - https://doi.org/10.1016/B978-1-4832-3211-9.50009-7 DO - 10.1016/B978-1-4832-3211-9.50009-7 ID - Jukes1969 ER - TY - JOUR AU - Kimura, M. PY - 1980 DA - 1980// TI - A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences JO - J Mol Evol VL - 16 UR - https://doi.org/10.1007/BF01731581 DO - 10.1007/BF01731581 ID - Kimura1980 ER - TY - JOUR AU - Kishino, H. AU - Hasegawa, M. PY - 1990 DA - 1990// TI - Converting distance to time: Application to human evolution JO - Methods in Enzymology VL - 183 UR - https://doi.org/10.1016/0076-6879(90)83036-9 DO - 10.1016/0076-6879(90)83036-9 ID - Kishino1990 ER - TY - JOUR AU - Hasegawa, M. AU - Kishino, H. AU - Yano, T. PY - 1985 DA - 1985// TI - Dating the human-ape splitting by a molecular clock of mitochondrial DNA JO - J Mol Evol VL - 22 UR - https://doi.org/10.1007/BF02101694 DO - 10.1007/BF02101694 ID - Hasegawa1985 ER - TY - JOUR AU - Tamura, K. AU - Nei, M. PY - 1993 DA - 1993// TI - Estimation of the number of nucleotide substitutions in the control region of nitochondrial DNA in humans and chimpanzees JO - Mol Biol Evol VL - 10 ID - Tamura1993 ER - TY - JOUR AU - Felsenstein, J. AU - Churchill, G. A. PY - 1996 DA - 1996// TI - A hidden Markov model approach to variation among sites in rate of evolution JO - Mol Biol Evol VL - 13 UR - https://doi.org/10.1093/oxfordjournals.molbev.a025575 DO - 10.1093/oxfordjournals.molbev.a025575 ID - Felsenstein1996 ER - TY - JOUR AU - Holmes, I. P. AU - Rubin, G. M. PY - 2002 DA - 2002// TI - An expectation maximization algorithm for training hidden substitution models JO - J Mol Biol VL - 317 UR - https://doi.org/10.1006/jmbi.2002.5405 DO - 10.1006/jmbi.2002.5405 ID - Holmes2002 ER - TY - JOUR AU - Nelder, J. A. AU - Mead, R. PY - 1965 DA - 1965// TI - A simplex method for function minimization JO - Comput J VL - 7 UR - https://doi.org/10.1093/comjnl/7.4.308 DO - 10.1093/comjnl/7.4.308 ID - Nelder1965 ER -