{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,11]],"date-time":"2026-06-11T03:44:04Z","timestamp":1781149444137,"version":"3.54.1"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2005,2]]},"DOI":"10.1093\/molbev\/msi005","type":"journal-article","created":{"date-parts":[[2004,10,14]],"date-time":"2004-10-14T00:24:51Z","timestamp":1097713491000},"page":"193-199","source":"Crossref","is-referenced-by-count":122,"title":["Different Versions of the Dayhoff Rate Matrix"],"prefix":"10.1093","volume":"22","author":[{"given":"Carolin","family":"Kosiol","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nick","family":"Goldman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2004,10,13]]},"reference":[{"key":"key\n\t\t\t\t20170418171500_BIB1","unstructured":"Adachi, J., and M. Hasegawa. 1992. MOLPHY version 2.3: Programs for Molecular Phylogenetics Based on Maximum Likelihood. Computer Science Monographs 28, Institute of Statistical Mathematics, Tokyo. http:\/\/www.ism.ac.jp\/software\/ismlib\/softother.e.html#molphy"},{"key":"key\n\t\t\t\t20170418171500_BIB2","doi-asserted-by":"crossref","unstructured":"\u2014\u2014\u2014. 1996. Model of amino acid substitution in proteins encoded by mitochondrial DNA. J. Mol. Evol.42:459\u2013468.","DOI":"10.1007\/BF02498640"},{"key":"key\n\t\t\t\t20170418171500_BIB3","doi-asserted-by":"crossref","unstructured":"Adachi, J., P. J. Waddell, W. Martin, and M. Hasegawa. 2000. Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA. J. Mol. Evol.50:348\u2013358.","DOI":"10.1007\/s002399910038"},{"key":"key\n\t\t\t\t20170418171500_BIB4","doi-asserted-by":"crossref","unstructured":"Cao, Y., J. Adachi, A. Janke, S. Pa\u0308a\u0308bo, and M. Hasegawa. 1994. Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: instability of a tree based on a single gene. J. Mol. Evol.39:519\u2013527.","DOI":"10.1007\/BF00173421"},{"key":"key\n\t\t\t\t20170418171500_BIB5","unstructured":"Dayhoff, M. O., R. V. Eck, and C. M. Park. 1972. A model of evolutionary change in proteins. Pp. 89\u201399 in M. O. Dayhoff, ed., Atlas of Protein Sequence and Structure Vol. 5. National Biomedical Research Foundation, Washington, D.C."},{"key":"key\n\t\t\t\t20170418171500_BIB6","unstructured":"Dayhoff, M. O., R. M. Schwartz, and B. C. Orcutt. 1978. A model of evolutionary change in proteins. Pp. 345\u2013352 in M. O. Dayhoff, ed., Atlas of Protein Sequence and Structure Vol. 5, suppl. 3. National Biomedical Research Foundation, Washington, D.C."},{"key":"key\n\t\t\t\t20170418171500_BIB7","doi-asserted-by":"crossref","unstructured":"Devauchelle, C., A. Grossmann, A. He\u0301naut, M. Holschneider, M. Monnerot, J. L. Riesler, and B. Torre\u0301sani. 2001. Rate matrices for analyzing large families of protein sequences. J. Comp. Biol.8:381\u2013399.","DOI":"10.1089\/106652701752236205"},{"key":"key\n\t\t\t\t20170418171500_BIB8","doi-asserted-by":"crossref","unstructured":"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\u201373.","DOI":"10.1007\/s00239-001-2304-y"},{"key":"key\n\t\t\t\t20170418171500_BIB9","doi-asserted-by":"crossref","unstructured":"Felsenstein, J. 1996. Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods. Methods Enzymol.266:418\u2013427.","DOI":"10.1016\/S0076-6879(96)66026-1"},{"key":"key\n\t\t\t\t20170418171500_BIB10","unstructured":"\u2014\u2014\u2014. 2002. PHYLIP (Phylogeny Inference Package) Version 3.6a. Department of Genome Sciences, University of Washington, Seattle, Wash. http:\/\/evolution.genetics.washington.edu\/phylip.html"},{"key":"key\n\t\t\t\t20170418171500_BIB11","unstructured":"\u2014\u2014\u2014. 2003. Inferring phylogenies. Sinauer Associates, Sunderland, Mass."},{"key":"key\n\t\t\t\t20170418171500_BIB12","doi-asserted-by":"crossref","unstructured":"Goldman, N., J. L. Thorne, and D. T. Jones. 1996. Using evolutionary trees in protein secondary structure prediction and other comparative sequence analysis. J. Mol. Biol.263:196\u2013208.","DOI":"10.1006\/jmbi.1996.0569"},{"key":"key\n\t\t\t\t20170418171500_BIB13","doi-asserted-by":"crossref","unstructured":"\u2014\u2014\u2014. 1998. Assessing the impact of secondary structure and solvent accessibility on protein evolution. Genetics149:445\u2013458.","DOI":"10.1093\/genetics\/149.1.445"},{"key":"key\n\t\t\t\t20170418171500_BIB14","doi-asserted-by":"crossref","unstructured":"Grassly, N. C., J. Adachi, and A. Rambaut. 1997. PSeq-Gen: an application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees. CABIOS13:559\u2013560. http:\/\/evolve.zoo.ox.ac.uk\/software.html?id=pseqgen","DOI":"10.1093\/bioinformatics\/13.5.559"},{"key":"key\n\t\t\t\t20170418171500_BIB15","doi-asserted-by":"crossref","unstructured":"Guindon, S., and O. Gascuel. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol.52:696\u2013704. http:\/\/atgc.lirmm.fr\/phyml","DOI":"10.1080\/10635150390235520"},{"key":"key\n\t\t\t\t20170418171500_BIB16","doi-asserted-by":"crossref","unstructured":"International Chimpanzee Chromosome 22 Consortium. 2004. DNA sequence and comparative analysis of chimpanzee chromosome 22. Nature429:382\u2013388.","DOI":"10.1038\/nature02564"},{"key":"key\n\t\t\t\t20170418171500_BIB17","doi-asserted-by":"crossref","unstructured":"International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature409:860\u2013921.","DOI":"10.1038\/35057062"},{"key":"key\n\t\t\t\t20170418171500_BIB18","unstructured":"International SNP Map Working Group. 2001. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature409:928\u2013933."},{"key":"key\n\t\t\t\t20170418171500_BIB19","doi-asserted-by":"crossref","unstructured":"Jones, D. T., W. R. Taylor, and J. M. Thornton. 1992. The rapid generation of mutation data matrices from protein sequences. CABIOS8:275\u2013282.","DOI":"10.1093\/bioinformatics\/8.3.275"},{"key":"key\n\t\t\t\t20170418171500_BIB20","doi-asserted-by":"crossref","unstructured":"Kishino, H., T. Miyata, and M. Hasegawa. 1990. Maximum likelihood inference of protein phylogeny and the origin of chloroplasts. J. Mol. Evol.31:151\u2013160.","DOI":"10.1007\/BF02109483"},{"key":"key\n\t\t\t\t20170418171500_BIB21","doi-asserted-by":"crossref","unstructured":"Lio\u0300, P., and N. Goldman. 1998. Models of molecular evolution and phylogeny. Genome Res.8:1233\u20131244.","DOI":"10.1101\/gr.8.12.1233"},{"key":"key\n\t\t\t\t20170418171500_BIB22","doi-asserted-by":"crossref","unstructured":"Moler, C., and C. Van Loan. 2003. Nineteen dubious ways to compute the exponential of a matrix, twenty-five years later. SIAM Rev.45:3\u201349.","DOI":"10.1137\/S00361445024180"},{"key":"key\n\t\t\t\t20170418171500_BIB23","doi-asserted-by":"crossref","unstructured":"Mouse Genome Sequencing Consortium. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature420:520\u2013562.","DOI":"10.1038\/nature01262"},{"key":"key\n\t\t\t\t20170418171500_BIB24","doi-asserted-by":"crossref","unstructured":"Mu\u0308ller, T., and M. Vingron. 2000. Modeling amino acid replacement. J. Comp. Biol.7:761\u2013776.","DOI":"10.1089\/10665270050514918"},{"key":"key\n\t\t\t\t20170418171500_BIB25","doi-asserted-by":"crossref","unstructured":"Rambaut, A., and N. C. Grassly. 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. CABIOS13:235\u2013238. http:\/\/evolve.zoo.ox.ac.uk\/software.html?id=seqgen","DOI":"10.1093\/bioinformatics\/13.3.235"},{"key":"key\n\t\t\t\t20170418171500_BIB26","doi-asserted-by":"crossref","unstructured":"Rat Genome Sequencing Project Consortium. 2004. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature428:493\u2013521.","DOI":"10.1038\/nature02426"},{"key":"key\n\t\t\t\t20170418171500_BIB27","doi-asserted-by":"crossref","unstructured":"Ronquist, F., and J. P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics19:1572\u20131574. http:\/\/morphbank.ebc.uu.se\/mrbayes3","DOI":"10.1093\/bioinformatics\/btg180"},{"key":"key\n\t\t\t\t20170418171500_BIB28","doi-asserted-by":"crossref","unstructured":"Schmidt, H. A., K. Strimmer, M. Vingron, and A. von Haeseler. 2002. Tree-Puzzle: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics18:502\u2013504. http:\/\/www.tree-puzzle.de","DOI":"10.1093\/bioinformatics\/18.3.502"},{"key":"key\n\t\t\t\t20170418171500_BIB29","unstructured":"Swofford, D. L. 2002. PAUP*. *Phylogenetic analysis using parsimony (and other methods) version 4. Sinauer Associates, Sunderland, Mass. http:\/\/paup.csit.fsu.edu"},{"key":"key\n\t\t\t\t20170418171500_BIB30","doi-asserted-by":"crossref","unstructured":"Thorne, J. L., and N. Goldman. 2003. Probabilistic models for the study of protein evolution. Pp. 209\u2013226 in D. J. Balding, M. Bishop, and C. Cannings, eds. Handbook of Statistical Genetics, 2nd Ed. Wiley, Chichester.","DOI":"10.1002\/0470022620.bbc05"},{"key":"key\n\t\t\t\t20170418171500_BIB31","doi-asserted-by":"crossref","unstructured":"Veerassamy, S., A. Smith, and E. R. M. Tillier. 2003. A transition probability model for amino acid substitutions from Blocks. J. Comp. Biol.10:997\u20131010.","DOI":"10.1089\/106652703322756195"},{"key":"key\n\t\t\t\t20170418171500_BIB32","doi-asserted-by":"crossref","unstructured":"Whelan, S., P. I. W. de Bakker, and N. Goldman. 2003. Pandit: a database of protein and associated nucleotide domains with inferred trees. Bioinformatics19:1556\u20131563. http:\/\/www.ebi.ac.uk\/goldman-srv\/pandit","DOI":"10.1093\/bioinformatics\/btg188"},{"key":"key\n\t\t\t\t20170418171500_BIB33","doi-asserted-by":"crossref","unstructured":"Whelan, S., and N. Goldman. 2001. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol. Biol. Evol.18:691\u2013699.","DOI":"10.1093\/oxfordjournals.molbev.a003851"},{"key":"key\n\t\t\t\t20170418171500_BIB34","doi-asserted-by":"crossref","unstructured":"Yang, Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. CABIOS13:555\u2013556. http:\/\/abacus.gene.ucl.ac.uk\/software\/paml.html","DOI":"10.1093\/bioinformatics\/13.5.555"},{"key":"key\n\t\t\t\t20170418171500_BIB35","doi-asserted-by":"crossref","unstructured":"Yang, Z., R. Nielsen, and M. Hasegawa. 1998. Models of amino acid substitution and applications to mitochondrial protein evolution. Mol. Biol. Evol.15:1600\u20131611.","DOI":"10.1093\/oxfordjournals.molbev.a025888"}],"container-title":["Molecular Biology and Evolution"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/mbe\/article-pdf\/22\/2\/193\/13432770\/msi005.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,1,14]],"date-time":"2024-01-14T16:56:26Z","timestamp":1705251386000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/mbe\/article-lookup\/doi\/10.1093\/molbev\/msi005"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2004,10,13]]},"references-count":35,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2004,10,13]]},"published-print":{"date-parts":[[2005,2]]}},"URL":"https:\/\/doi.org\/10.1093\/molbev\/msi005","relation":{},"ISSN":["1537-1719","0737-4038"],"issn-type":[{"value":"1537-1719","type":"electronic"},{"value":"0737-4038","type":"print"}],"subject":[],"published":{"date-parts":[[2004,10,13]]}}}