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 - Thompson, J. AU - Higgins, D. AU - Gibson, T. PY - 1994 DA - 1994// TI - CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice JO - Nucl Acids Res VL - 22 UR - https://doi.org/10.1093/nar/22.22.4673 DO - 10.1093/nar/22.22.4673 ID - Thompson1994 ER - TY - CHAP AU - Jukes, T. H. AU - Cantor, C. ED - Munro, H. N. PY - 1969 DA - 1969// TI - Evolution of protein molecules BT - Mammalian Protein Metabolism PB - Academic Press CY - New York 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 - Hasegawa, M. AU - Kishino, H. AU - Yano, T. PY - 1985 DA - 1985// TI - Dating of 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 - BOOK AU - Nei, M. AU - Kumar, S. PY - 2000 DA - 2000// TI - Molecular evolution and phylogenetics PB - Oxford University Press CY - Oxford, UK ID - Nei2000 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 - Tavare, S. PY - 1986 DA - 1986// TI - Some probabilistic and statistical problems in the analysis of DNA sequences JO - Lectures on Mathematics in the Life Sciences VL - 17 ID - Tavare1986 ER - TY - JOUR AU - Rodriguez, F. AU - Oliver, J. L. AU - Marin, A. AU - Medina, J. R. PY - 1990 DA - 1990// TI - The general stochastic model of nucleotide substitution JO - J Theor Biol VL - 142 UR - https://doi.org/10.1016/S0022-5193(05)80104-3 DO - 10.1016/S0022-5193(05)80104-3 ID - Rodriguez1990 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 - Steel, M. A. PY - 1994 DA - 1994// TI - Recovering a tree from the leaf colourations it generates under a Markov model JO - Appl Math Lett VL - 7 UR - https://doi.org/10.1016/0893-9659(94)90024-8 DO - 10.1016/0893-9659(94)90024-8 ID - Steel1994 ER - TY - JOUR AU - Lake, J. A. PY - 1994 DA - 1994// TI - Reconstructing evolutionary trees from DNA and protein sequences: paralinear distances JO - Proc Natl Acad Sci USA VL - 91 UR - https://doi.org/10.1073/pnas.91.4.1455 DO - 10.1073/pnas.91.4.1455 ID - Lake1994 ER - TY - JOUR AU - Nei, M. AU - Gojobori, T. PY - 1986 DA - 1986// TI - Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions JO - Mol Biol Evol VL - 3 ID - Nei1986 ER - TY - JOUR AU - Li, W. H. AU - Wu, C. I. AU - Luo, C. C. PY - 1985 DA - 1985// TI - A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes JO - Mol Biol Evol VL - 2 ID - Li1985 ER - TY - JOUR AU - Li, W. H. PY - 1993 DA - 1993// TI - Unbiased estimation of the rates of synonymous and nonsynonymous substitution JO - J Mol Evol VL - 36 UR - https://doi.org/10.1007/BF02407308 DO - 10.1007/BF02407308 ID - Li1993 ER - TY - JOUR AU - Pamilo, P. AU - Bianchi, N. O. PY - 1993 DA - 1993// TI - Evolution of the Zfx and Zfy genes: rates and interdependence between the genes JO - Mol Biol Evol VL - 10 ID - Pamilo1993 ER - TY - BOOK AU - Yang, Z. PY - 2000 DA - 2000// TI - Phylogenetic Analysis by Maximum Likelihood (PAML). Version 3.0 PB - University College CY - London ID - Yang2000 ER - TY - JOUR AU - Saitou, N. AU - Nei, M. 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 - 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 - Rzhetsky, A. AU - Morozov, P. PY - 2001 DA - 2001// TI - Markov chain Monte Carlo computation of confidence intervals for substitution-rate variation in proteins JO - Pac Symp Biocomput VL - 6 ID - Rzhetsky2001 ER - TY - JOUR AU - Plotkin, J. B. AU - Dushoff, J. AU - Fraser, H. B. PY - 2004 DA - 2004// TI - Detecting selection using a single genome sequence of M. tuberculosis and P. falciparum JO - Nature VL - 428 UR - https://doi.org/10.1038/nature02458 DO - 10.1038/nature02458 ID - Plotkin2004 ER - TY - JOUR AU - Zhang, R. AU - Zhang, C. T. PY - 1994 DA - 1994// TI - Z curves, an intutive tool for visualizing and analyzing the DNA sequences JO - J Biomol Struct Dyn VL - 11 UR - https://doi.org/10.1080/07391102.1994.10508031 DO - 10.1080/07391102.1994.10508031 ID - Zhang1994 ER - TY - JOUR AU - Pearson, W. R. AU - Lipman, D. J. PY - 1988 DA - 1988// TI - Improved tools for biological sequence comparison JO - Proc Natil Acad Sci U S A VL - 85 UR - https://doi.org/10.1073/pnas.85.8.2444 DO - 10.1073/pnas.85.8.2444 ID - Pearson1988 ER - TY - JOUR AU - Smith, T. F. AU - Waterman, M. S. PY - 1981 DA - 1981// TI - Identification of common molecular subsequences JO - J Mol Biol VL - 147 UR - https://doi.org/10.1016/0022-2836(81)90087-5 DO - 10.1016/0022-2836(81)90087-5 ID - Smith1981 ER - TY - JOUR AU - Venet, D. PY - 2003 DA - 2003// TI - MatArray: a Matlab toolbox for microarray data JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg046 DO - 10.1093/bioinformatics/btg046 ID - Venet2003 ER - TY - STD TI - MATLAB Central[http://www.mathworks.com/matlabcentral/] UR - http://www.mathworks.com/matlabcentral/ ID - ref26 ER - TY - JOUR AU - Sharp, P. M. PY - 1997 DA - 1997// TI - In search of molecular darwinism JO - Nature VL - 385 UR - https://doi.org/10.1038/385111a0 DO - 10.1038/385111a0 ID - Sharp1997 ER - TY - JOUR AU - Akashi, H. PY - 1999 DA - 1999// TI - Within- and between-species DNA sequence variation and the 'footprint' of natural selection JO - Gene VL - 238 UR - https://doi.org/10.1016/S0378-1119(99)00294-2 DO - 10.1016/S0378-1119(99)00294-2 ID - Akashi1999 ER - TY - JOUR AU - Crandall, K. AU - Kelsey, C. AU - Imamichi, H. AU - Lane, H. AU - Salzman, N. PY - 1999 DA - 1999// TI - Parallel evolution of drug resistance in HIV: failure of nonsynonymous/synonymous substitution rate ratio to detect selection JO - Mol Biol Evol VL - 16 UR - https://doi.org/10.1093/oxfordjournals.molbev.a026118 DO - 10.1093/oxfordjournals.molbev.a026118 ID - Crandall1999 ER - TY - JOUR AU - Clark, A. G. AU - Kao, T. PY - 1991 DA - 1991// TI - Nonsynonymous Substitution at Shared Polymorphic Sites Among Self-Incompatibility Alleles of Solanaceae JO - Proc Natl Acad Sci USA VL - 88 UR - https://doi.org/10.1073/pnas.88.21.9823 DO - 10.1073/pnas.88.21.9823 ID - Clark1991 ER - TY - JOUR AU - Ina, Y. PY - 1994 DA - 1994// TI - ODEN: a program package for molecular evolutionary analysis and database search of DNA and amino acid sequences JO - Comput Appl Biosci VL - 10 ID - Ina1994 ER - TY - JOUR AU - Endo, T. AU - Ikeo, K. AU - Gojobori, T. PY - 1996 DA - 1996// TI - Large-scale search for genes on which positive selection may operate JO - Mol Biol Evol VL - 13 UR - https://doi.org/10.1093/oxfordjournals.molbev.a025629 DO - 10.1093/oxfordjournals.molbev.a025629 ID - Endo1996 ER - TY - JOUR AU - Choi, S. S. AU - Lahn, B. T. PY - 2003 DA - 2003// TI - Adaptive evolution of MRG, a neuron-specific gene family implicated in nociception JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.1431603 DO - 10.1101/gr.1431603 ID - Choi2003 ER - TY - JOUR AU - Zhang, C. T. AU - Wang, J. AU - Zhang, R. PY - 2001 DA - 2001// TI - A novel method to calculate the G+C content of genomic DNA sequences JO - J Biomol Struct Dyn VL - 19 UR - https://doi.org/10.1080/07391102.2001.10506743 DO - 10.1080/07391102.2001.10506743 ID - Zhang2001 ER - TY - CHAP AU - Suzuki, Y. AU - Gojobori, T. ED - Salemi, M. ED - Vandamme, A. PY - 2003 DA - 2003// TI - Analysis of coding sequences BT - The phylogenetic handbook: a practical approach to DNA and protein phylogeny PB - Cambridge University Press CY - Cambridge, UK ID - Suzuki2003 ER -