{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,5]],"date-time":"2024-09-05T12:57:11Z","timestamp":1725541031002},"publisher-location":"Berlin, Heidelberg","reference-count":45,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783642111686"},{"type":"electronic","value":"9783642111693"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009]]},"DOI":"10.1007\/978-3-642-11169-3_19","type":"book-chapter","created":{"date-parts":[[2009,11,27]],"date-time":"2009-11-27T16:26:05Z","timestamp":1259339165000},"page":"259-272","source":"Crossref","is-referenced-by-count":1,"title":["Substitution Matrices and Mutual Information Approaches to Modeling Evolution"],"prefix":"10.1007","author":[{"given":"Stephan","family":"Kitchovitch","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuedong","family":"Song","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Richard","family":"van der Wath","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pietro","family":"Li\u00f2","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"key":"19_CR1","doi-asserted-by":"publisher","first-page":"459","DOI":"10.1007\/BF02498640","volume":"42","author":"J. Adachi","year":"1996","unstructured":"Adachi, J., Hasegawa, M.: Model of amino acid substitution in proteins encoded by mitochondrial DNA. J. Mol. Evol.\u00a042, 459\u2013468 (1996a)","journal-title":"J. Mol. Evol."},{"key":"19_CR2","doi-asserted-by":"publisher","first-page":"407","DOI":"10.1093\/bioinformatics\/btg427","volume":"20","author":"G. Altekar","year":"2004","unstructured":"Altekar, G., Dwarkadas, S., Huelsenbeck, J.P., Ronquist, F.: Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics\u00a020, 407\u2013415 (2004)","journal-title":"Bioinformatics"},{"key":"19_CR3","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/molbev\/msl136","volume":"24","author":"F. Abascal","year":"2007","unstructured":"Abascal, F., Posada, D., Zardoya, R.: MtArt: a new model of amino acid replacement for Arthropoda. Mol. Biol. Evol.\u00a024, 1\u20135 (2007)","journal-title":"Mol. Biol. Evol."},{"key":"19_CR4","doi-asserted-by":"publisher","first-page":"754","DOI":"10.1093\/bioinformatics\/17.8.754","volume":"17","author":"J.P. Huelsenbeck","year":"2001","unstructured":"Huelsenbeck, J.P., Ronquist, F.: MrBayes: Bayesian inference in phylogenetic trees. Bioinformatics\u00a017, 754\u2013755 (2001)","journal-title":"Bioinformatics"},{"key":"19_CR5","doi-asserted-by":"publisher","first-page":"1572","DOI":"10.1093\/bioinformatics\/btg180","volume":"19","author":"F. Ronquist","year":"2003","unstructured":"Ronquist, F., Huelsenbeck, J.P.: MrBayes3: Bayesian phylogenetic inference under mixed models. Bioinformatics\u00a019, 1572\u20131574 (2003)","journal-title":"Bioinformatics"},{"key":"19_CR6","doi-asserted-by":"crossref","first-page":"1645","DOI":"10.1093\/genetics\/164.4.1645","volume":"164","author":"B. Rannala","year":"2003","unstructured":"Rannala, B., Yang, Z.: Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics\u00a0164, 1645\u20131656 (2003)","journal-title":"Genetics"},{"key":"19_CR7","doi-asserted-by":"publisher","first-page":"196","DOI":"10.1006\/jmbi.1996.0569","volume":"263","author":"N. Goldman","year":"1996","unstructured":"Goldman, N., Thorne, J.L., Jones, D.T.: Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses. J. Mol. Biol.\u00a0263, 196\u2013208 (1996)","journal-title":"J. Mol. Biol."},{"key":"19_CR8","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1093\/genetics\/149.1.445","volume":"149","author":"N. Goldman","year":"1998","unstructured":"Goldman, N., Thorne, J.L., Jones, D.T.: Assessing the impact of secondary structure and solvent accessibility on protein evolution. Genetics\u00a0149, 445\u2013458 (1998)","journal-title":"Genetics"},{"key":"19_CR9","doi-asserted-by":"crossref","first-page":"1696","DOI":"10.1093\/oxfordjournals.molbev.a026083","volume":"16","author":"P. Li\u00f2","year":"1999","unstructured":"Li\u00f2, P., Goldman, N.: Using protein structural information in evolutionary inference: transmembrane proteins. Mol. Biol. Evol.\u00a016, 1696\u20131710 (1999)","journal-title":"Mol. Biol. Evol."},{"key":"19_CR10","first-page":"275","volume":"8","author":"D.T. Jones","year":"1992","unstructured":"Jones, D.T., Taylor, W.R., Thornton, J.M.: The rapid generation of mutation data matrices from protein sequences. CABIOS\u00a08, 275\u2013282 (1992)","journal-title":"CABIOS"},{"key":"19_CR11","doi-asserted-by":"publisher","first-page":"269","DOI":"10.1016\/0014-5793(94)80429-X","volume":"339","author":"D.T. Jones","year":"1994","unstructured":"Jones, D.T., Taylor, W.R., Thornton, J.M.: A mutation data matrix for transmembrane proteins. FEBS Letts\u00a0339, 269\u2013275 (1994)","journal-title":"FEBS Letts"},{"key":"19_CR12","doi-asserted-by":"publisher","first-page":"555","DOI":"10.1016\/0022-2836(91)90193-A","volume":"219","author":"S.F. Altschul","year":"1991","unstructured":"Altschul, S.F.: Amino acid substitutions matrices from an information theoretic perspective. J. Mol. Biol.\u00a0219, 555\u2013665 (1991)","journal-title":"J. Mol. Biol."},{"key":"19_CR13","unstructured":"Dayhoff, M.O., Schwartz, R.M., Orcutt, B.C.: A model of evolutionary change in proteins. In: Dayhoff, M.O. (ed.) Atlas of Protein Sequence and Structure, vol.\u00a05(3), pp. 345\u2013352 (1978)"},{"issue":"biochemistry","key":"19_CR14","doi-asserted-by":"publisher","first-page":"10915","DOI":"10.1073\/pnas.89.22.10915","volume":"89","author":"S. Henikoff","year":"1992","unstructured":"Henikoff, S., Henikoff, J.: Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA\u00a089(biochemistry), 10915\u201310919 (1992)","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"19_CR15","doi-asserted-by":"publisher","first-page":"262","DOI":"10.1016\/S0168-9525(01)02272-7","volume":"17","author":"S. Whelan","year":"2001","unstructured":"Whelan, S., Li\u00f2, P., Goldman, N.: Molecular phylogenetics: State-of-art methods for looking into the past. Trends Genet.\u00a017, 262\u2013272 (2001)","journal-title":"Trends Genet."},{"key":"19_CR16","doi-asserted-by":"crossref","first-page":"1233","DOI":"10.1101\/gr.8.12.1233","volume":"8","author":"P. Li\u00f2","year":"1998","unstructured":"Li\u00f2, P., Goldman, N.: Models of molecular evolution and phylogeny. Genome Res.\u00a08, 1233\u20131244 (1998)","journal-title":"Genome Res."},{"key":"19_CR17","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1023\/A:1010791204961","volume":"133","author":"A. Chomyn","year":"2001","unstructured":"Chomyn, A.: Mitochondrial genetic control of assembly and function of complex I in mammalian cells. J. Bioenerg. Biomembr.\u00a0133, 251\u2013257 (2001)","journal-title":"J. Bioenerg. Biomembr."},{"key":"19_CR18","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1111\/j.1469-7793.2000.00057.x","volume":"529","author":"M.R. Duchen","year":"2000","unstructured":"Duchen, M.R.: Mitochondria and calcium: from cell signalling to cell death. J. Physiol.\u00a0529, 57\u201368 (2000)","journal-title":"J. Physiol."},{"key":"19_CR19","doi-asserted-by":"publisher","first-page":"862","DOI":"10.1126\/science.185.4154.862","volume":"185","author":"R. Grantham","year":"1974","unstructured":"Grantham, R.: Amino acid difference formula to help explain protein evolution. Science\u00a0185, 862\u2013864 (1974)","journal-title":"Science"},{"key":"19_CR20","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1093\/bioinformatics\/17.2.149","volume":"17","author":"M. Li","year":"2001","unstructured":"Li, M., Badger, J.H., Chen, X., Kwong, S., Kearney, P., Zhang, H.: An information-based sequence distance and its application to whole mitochondrial genome phylogeny. Bioinformatics\u00a017, 149\u2013154 (2001)","journal-title":"Bioinformatics"},{"key":"19_CR21","doi-asserted-by":"crossref","unstructured":"Carapelli, A., Li\u00f2, P., Nardi, F., van der Wath, E., Frati, F.: Phylogenetic analysis of mitochondrial protein coding genes confirms the reciprocal paraphyly of Hexapoda and Crustacea. BMC Evol. Biol.\u00a07(suppl. 2), S8 (2007)","DOI":"10.1186\/1471-2148-7-S2-S8"},{"key":"19_CR22","unstructured":"Li, M., Chen, X., Li, X., Ma, B., Vitanyi, P.: The similarity metric. E-print, arxiv.org\/cs.CC\/0111054 (2002)"},{"key":"19_CR23","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4757-2606-0","volume-title":"An introduction to Kolmogorov complexity and its applications","author":"M. Li","year":"1997","unstructured":"Li, M., Vitanyi, P.: An introduction to Kolmogorov complexity and its applications. Springer, New York (1997)"},{"key":"19_CR24","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1093\/oxfordjournals.molbev.a025661","volume":"13","author":"R. Zardoya","year":"1996","unstructured":"Zardoya, R., Meyer, A.: Phylogenetic performance of mitochondrial protein-coding genes in resolving relationships among vertebrates. Molecular Biology and Evolution\u00a013, 525\u2013536 (1996)","journal-title":"Molecular Biology and Evolution"},{"key":"19_CR25","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1016\/j.gene.2004.11.033","volume":"345","author":"P. Li\u00f2","year":"1999","unstructured":"Li\u00f2, P.: Phylogenetic and structural analysis of mitochondrial complex I proteins. Gene\u00a0345, 55\u201364 (1999)","journal-title":"Gene"},{"key":"19_CR26","doi-asserted-by":"crossref","first-page":"750","DOI":"10.1093\/oxfordjournals.molbev.a026160","volume":"16","author":"B. Larget","year":"1999","unstructured":"Larget, B., Simon, D.: Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. Evol.\u00a016, 750\u2013759 (1999)","journal-title":"Mol. Biol. Evol."},{"key":"19_CR27","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1111\/j.0006-341X.1999.00001.x","volume":"55","author":"B. Mau","year":"1999","unstructured":"Mau, B., Newton, M.A., Larget, B.: Bayesian phylogenetic inference via Markov chain Monte Carlo methods. Biometrics\u00a055, 1\u201312 (1999)","journal-title":"Biometrics"},{"key":"19_CR28","doi-asserted-by":"crossref","first-page":"717","DOI":"10.1093\/oxfordjournals.molbev.a025811","volume":"14","author":"Z. Yang","year":"1997","unstructured":"Yang, Z., Rannala, B.: Bayesian phylogenetic inference using DNA sequences: Markov chain Monte Carlo methods. Mol. Biol. Evol.\u00a014, 717\u2013724 (1997)","journal-title":"Mol. Biol. Evol."},{"key":"19_CR29","doi-asserted-by":"crossref","first-page":"1600","DOI":"10.1093\/oxfordjournals.molbev.a025888","volume":"15","author":"Z. Yang","year":"1998","unstructured":"Yang, Z., Nielsen, R., Hasegawa: Models of amino acid substitutions and applications to mitochondrial protein evolution. Mol. Biol. Evol.\u00a015, 1600\u20131611 (1998)","journal-title":"Mol. Biol. Evol."},{"key":"19_CR30","volume-title":"Mathematics of Evolution and Phylogeny","author":"O. Gascuel","year":"2007","unstructured":"Gascuel, O.: Mathematics of Evolution and Phylogeny. Oxford University Press, USA (2007)"},{"key":"19_CR31","series-title":"Oxford Series in Ecology and Evolution","doi-asserted-by":"crossref","DOI":"10.1093\/acprof:oso\/9780198567028.001.0001","volume-title":"Computational Molecular Evolution","author":"Z. Yang","year":"2006","unstructured":"Yang, Z.: Computational Molecular Evolution. Oxford Series in Ecology and Evolution. Oxford University Press, USA (2006)"},{"key":"19_CR32","unstructured":"Felsenstein, J.: Inferring Phylogenies, 2nd edn. Sinauer Associates (2003)"},{"key":"19_CR33","series-title":"Statistics for Biology and Health","doi-asserted-by":"crossref","DOI":"10.1007\/0-387-27733-1","volume-title":"Statistical Methods in Molecular Evolution","author":"R. Nielsen","year":"2005","unstructured":"Nielsen, R.: Statistical Methods in Molecular Evolution, 1st edn. Statistics for Biology and Health. Springer, Heidelberg (2005)","edition":"1"},{"key":"19_CR34","doi-asserted-by":"crossref","first-page":"1233","DOI":"10.1101\/gr.8.12.1233","volume":"8","author":"P. Li\u00f2","year":"1998","unstructured":"Li\u00f2, P., Goldman, N.: Models of molecular evolution and phylogeny. Genome Res.\u00a08, 1233\u20131244 (1998)","journal-title":"Genome Res."},{"key":"19_CR35","doi-asserted-by":"crossref","first-page":"933","DOI":"10.1093\/oxfordjournals.molbev.a025613","volume":"13","author":"C.A. Russo","year":"1996","unstructured":"Russo, C.A., Takezaki, N., Nei, M.: Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny. Mol. Biol. Evol.\u00a013, 933\u2013942 (1996)","journal-title":"Mol. Biol. Evol."},{"key":"19_CR36","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1007\/PL00006389","volume":"47","author":"Y. Cao","year":"1998","unstructured":"Cao, Y., Janke, A., Waddell, P.J., Westerman, M., Takenaka, O., Murata, S., Okada, N., Paabo, S., Hasegawa, M.: Conflict among individual mitochondrial proteins in resolving the phylogeny of eutherian orders. J. Mol. Evol.\u00a047, 307\u2013322 (1998)","journal-title":"J. Mol. Evol."},{"key":"19_CR37","first-page":"407","volume-title":"Molecular Systematics","author":"D.L. Swofford","year":"1996","unstructured":"Swofford, D.L., Olsen, G.J., Waddell, P.J., Hillis, D.M.: Phylogenetic inference. In: Hillis, D.M., Moritz, C., Mable, B.K. (eds.) Molecular Systematics, pp. 407\u2013514. Sinauer, Sunderland (1996)"},{"key":"19_CR38","doi-asserted-by":"publisher","first-page":"557","DOI":"10.1007\/PL00006412","volume":"47","author":"X. Xia","year":"1998","unstructured":"Xia, X., Li, W.H.: What amino acid properties affect protein evolution? J. Mol. Evol.\u00a047, 557\u2013564 (1998)","journal-title":"J. Mol. Evol."},{"key":"19_CR39","doi-asserted-by":"publisher","first-page":"306","DOI":"10.1007\/BF00160154","volume":"39","author":"Z. Yang","year":"1994","unstructured":"Yang, Z.: Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol.\u00a039, 306\u2013314 (1994)","journal-title":"J. Mol. Evol."},{"issue":"2","key":"19_CR40","doi-asserted-by":"publisher","first-page":"151","DOI":"10.1006\/jtbi.1996.0091","volume":"180","author":"P. Li\u00f2","year":"1996","unstructured":"Li\u00f2, P., Politi, A., Buiatti, M., Ruffo, S.: High statistics block entropy measures of DNA sequences. J. Theor. Biol.\u00a0180(2), 151\u2013160 (1996)","journal-title":"J. Theor. Biol."},{"issue":"6 Pt 2","key":"19_CR41","doi-asserted-by":"crossref","first-page":"066138","DOI":"10.1103\/PhysRevE.69.066138","volume":"69","author":"A. Kraskov","year":"2004","unstructured":"Kraskov, A., St\u00f6gbauer, H., Grassberger, P.: Estimating mutual information. Phys. Rev. E Stat. Nonlin. Soft. Matter. Phys.\u00a069(6 Pt 2), 066138 (2004)","journal-title":"Phys. Rev. E Stat. Nonlin. Soft. Matter. Phys."},{"key":"19_CR42","first-page":"349","volume":"25","author":"J. Hein","year":"1994","unstructured":"Hein, J.: TreeAlign. Methods Mol. Biol.\u00a025, 349\u2013364 (1994)","journal-title":"Methods Mol. Biol."},{"key":"19_CR43","doi-asserted-by":"publisher","first-page":"519","DOI":"10.1007\/s00239-007-9030-z","volume":"65","author":"C. Papetti","year":"2007","unstructured":"Papetti, C., Li\u00f2, P., Ruber, L., Patarnello, T., Zardoya, R.: Antarctic Fish Mitochondrial Genomes Lack ND6. Gene J. Mol. Evol.\u00a065, 519\u2013528 (2007)","journal-title":"Gene J. Mol. Evol."},{"key":"19_CR44","volume-title":"Biometry","author":"R.R. Sokal","year":"1995","unstructured":"Sokal, R.R., Rohlf, F.J.: Biometry, 3rd edn. Freeman, New York (1995)","edition":"3"},{"key":"19_CR45","unstructured":"Seq-Gen: a program that will simulate the evolution of nucleotide or amino acid sequences along a phylogeny, http:\/\/tree.bio.ed.ac.uk\/software\/seqgen\/"}],"container-title":["Lecture Notes in Computer Science","Learning and Intelligent Optimization"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-642-11169-3_19","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,10,14]],"date-time":"2021-10-14T18:13:00Z","timestamp":1634235180000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-642-11169-3_19"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009]]},"ISBN":["9783642111686","9783642111693"],"references-count":45,"URL":"https:\/\/doi.org\/10.1007\/978-3-642-11169-3_19","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2009]]}}}