MBEToolbox: a Matlab toolbox for sequence data analysis in molecular biology and evolution
暂无分享,去创建一个
David K. Smith | Xuhua Xia | James J. Cai | Kwok-Yung Yuen | James J. Cai | K. Yuen | D. Smith | X. Xia
[1] D. Lipman,et al. Improved tools for biological sequence comparison. , 1988, Proceedings of the National Academy of Sciences of the United States of America.
[2] T. Jukes. CHAPTER 24 – Evolution of Protein Molecules , 1969 .
[3] Joshua B. Plotkin,et al. Detecting selection using a single genome sequence of M. tuberculosis and P. falciparum , 2004, Nature.
[4] Wen-Hsiung Li. Unbiased estimation of the rates of synonymous and nonsynonymous substitution , 2006, Journal of Molecular Evolution.
[5] M. Nei,et al. Molecular Evolution and Phylogenetics , 2000 .
[6] R Zhang,et al. Z curves, an intutive tool for visualizing and analyzing the DNA sequences. , 1994, Journal of biomolecular structure & dynamics.
[7] C. Luo,et al. A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. , 1985, Molecular biology and evolution.
[8] H. Kishino,et al. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA , 2005, Journal of Molecular Evolution.
[9] Andrey Rzhetsky,et al. Markov Chain Monte Carlo Computation of Confidence Intervals for Substitution-Rate Variation in Proteins , 2000, Pacific Symposium on Biocomputing.
[10] J. Thompson,et al. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.
[11] Ziheng Yang. Estimating the pattern of nucleotide substitution , 1994, Journal of Molecular Evolution.
[12] N. Bianchi,et al. Evolution of the Zfx and Zfy genes: rates and interdependence between the genes. , 1993, Molecular biology and evolution.
[13] Y. Ina,et al. ODEN: a program package for molecular evolutionary analysis and database search of DNA and amino acid sequences , 1994, Comput. Appl. Biosci..
[14] M. Nei,et al. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. , 1986, Molecular biology and evolution.
[15] M S Waterman,et al. Identification of common molecular subsequences. , 1981, Journal of molecular biology.
[16] S. Jeffery. Evolution of Protein Molecules , 1979 .
[17] M. Steel. Recovering a tree from the leaf colourations it generates under a Markov model , 1994 .
[18] M. Salemi,et al. The phylogenetic handbook : a practical approach to DNA and protein phylogeny , 2003 .
[19] R Zhang,et al. A Novel Method to Calculate the G+C Content of Genomic DNA Sequences , 2001, Journal of biomolecular structure & dynamics.
[20] G. Serio,et al. A new method for calculating evolutionary substitution rates , 2005, Journal of Molecular Evolution.
[21] J. Oliver,et al. The general stochastic model of nucleotide substitution. , 1990, Journal of theoretical biology.
[22] T Gojobori,et al. Large-scale search for genes on which positive selection may operate. , 1996, Molecular biology and evolution.
[23] K. Crandall,et al. Parallel evolution of drug resistance in HIV: failure of nonsynonymous/synonymous substitution rate ratio to detect selection. , 1999, Molecular biology and evolution.
[24] N. Saitou,et al. The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.
[25] Bruce T Lahn,et al. Adaptive evolution of MRG, a neuron-specific gene family implicated in nociception. , 2003, Genome research.
[26] M. Kimura. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences , 1980, Journal of Molecular Evolution.
[27] J. Lake,et al. Reconstructing evolutionary trees from DNA and protein sequences: paralinear distances. , 1994, Proceedings of the National Academy of Sciences of the United States of America.
[28] J. Felsenstein. Evolutionary trees from DNA sequences: A maximum likelihood approach , 2005, Journal of Molecular Evolution.
[29] S. Tavaré. Some probabilistic and statistical problems in the analysis of DNA sequences , 1986 .
[30] H. Akashi,et al. Within- and between-species DNA sequence variation and the 'footprint' of natural selection. , 1999, Gene.
[31] H. Munro,et al. Mammalian protein metabolism , 1964 .
[32] A. Clark,et al. Excess nonsynonymous substitution of shared polymorphic sites among self-incompatibility alleles of Solanaceae. , 1991, Proceedings of the National Academy of Sciences of the United States of America.
[33] P. Sharp,et al. In search of molecular darwinism , 1997, Nature.
[34] David Venet,et al. MatArray: a Matlab toolbox for microarray data , 2003, Bioinform..
[35] Ziheng Yang,et al. Phylogenetic Analysis by Maximum Likelihood (PAML) , 2002 .