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2007 年 11 月 3 日 改訂
井上 潤 |
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アミノ酸置換行列に関する個人的なメモです. |
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Lio, P., and N. Goldman. 2006. Models of Molecular Evolution and Phylogeny. Genome Research 8: 1233-1244.
Yang, Z. 2006. Computational Molecular Evolution. Oxford University Press, Oxford. Dimmic, M. W. 2005. Markov models of protein sequence evolution. Pages 259-287 in Statistical Methods in Molecular Evolution (R. Nielsen, ed.) Springer, New York. |
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mtREV24
Adachi, J., and M. Hasegawa. 1996. Model of amino acid substitution in proteins encoded by mitochondrial DNA. J Mol Evol 42: 459-468. Adachi, J., and M. Hasegawa. 1996. MOLPHY version 2.3: programs for molecular phylogenetics based on maximum likelihood. Computer Science Monographs of Institute of Statistical Mathematics 28: 1-150.
MTMAM, Cao, Y., A. Janke, P. J. Waddell, M. Westerman, O. Takenaka, S. Murata, N. Okada, S. Paabo, and M. Hasegawa. 1998. Conflict Among Individual Mitochondrial Proteins in Resolving the Phylogeny of Eutherian Orders. J. Mol. Evol. 47: 307-322. Yang, Z. H., R. Nielsen, and M. Hasegawa. 1998. Models of amino acid substitution and applications to mitochondrial protein evolution. Mol Biol Evol 15: 1600-1611.
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DAYHOFF
Dayhoff, M., R. Schwartz, and O. BC. 1978. A model of evolutionary change in proteins. Pages 345-352 in Atlas of protein sequence and structure. Vol. 5, Suppl. 3. National Biomedical Research Foundation, Washington, D.C.
JTT Jones, D. T., W. R. Taylor, and J. M. Thornton. 1992. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8: 275-282.
tmREV D. T. Jones, W. R. Taylor, and J. M. Thornton. A mutation data matrix for transmembrane proteins. FEBS Lett, 339(3):269. V275, Feb 1994.
WAG
RTREV Dimmic, M. W., J. S. Rest, D. P. Mindell, and R. A. Goldstein. 2002. rtREV: an amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny. J Mol Evol 55: 65-73.
VT Muller T, Vingron M Modeling amino acid replacement JOURNAL OF COMPUTATIONAL BIOLOGY 7 (6): 761-776 2000 website Muller T, Spang R, Vingron M Estimating amino acid substitution models: A comparison of Dayhoff's estimator, the resolvent approach and a maximum likelihood method MOLECULAR BIOLOGY AND EVOLUTION 19 (1): 8-13 JAN 2002 BLOSUM62 Henikoff, and Henikoff. 1992. Amino acid substitution matrices from protein blocksin Proc. Natl. Acad. Sci.
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CPREV
Adachi, J., P. Waddell, W. Martin, and M. Hasegawa. 2000. Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA. Journal of Molecular Evolution 50:348-358. |
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