Substitution model (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "Substitution model" in English language version.

refsWebsite

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80nih.gov

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67doi.org

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20harvard.edu

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12semanticscholar.org

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7worldcat.org

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4oup.com

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1wired.com

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1usc.edu

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1phylosolutions.com

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1psu.edu

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1books.google.com

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1cornell.edu

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1atgc-montpellier.fr

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1handle.net

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1jstor.org

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1ms609.github.io

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atgc-montpellier.fr (Global: low place; English: low place)

"ATGC: CAT". www.atgc-montpellier.fr.

books.google.com (Global: 3^rd place; English: 3^rd place)

Dayhoff MO, Eck RV, Park CM (1969). "A model of evolutionary change in proteins". In Dayhoff MO (ed.). Atlas of Protein Sequence and Structure. Vol. 4. pp. 75–84.

cornell.edu (Global: 332^nd place; English: 246^th place)

chagall.med.cornell.edu

Dayhoff MO, Schwartz RM, Orcutt BC (1978). "A model of evolutionary change in proteins" (PDF). In Dayhoff MO (ed.). Atlas of Protein Sequence and Structure. Vol. 5. pp. 345–352.

doi.org (Global: 2^nd place; English: 2^nd place)

Yang Z (July 1994). "Estimating the pattern of nucleotide substitution". Journal of Molecular Evolution. 39 (1): 105–111. Bibcode:1994JMolE..39..105Y. doi:10.1007/BF00178256. PMID 8064867. S2CID 15895455.
Jukes TH, Cantor CH (1969). "Evolution of Protein Molecules". In Munro HN (ed.). Mammalian Protein Metabolism. Vol. 3. Elsevier. pp. 21–132. doi:10.1016/b978-1-4832-3211-9.50009-7. ISBN 978-1-4832-3211-9.
Felsenstein J (November 1981). "Evolutionary trees from DNA sequences: a maximum likelihood approach". Journal of Molecular Evolution. 17 (6): 368–376. Bibcode:1981JMolE..17..368F. doi:10.1007/BF01734359. PMID 7288891. S2CID 8024924.
Kimura M (December 1980). "A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences". Journal of Molecular Evolution. 16 (2): 111–120. Bibcode:1980JMolE..16..111K. doi:10.1007/BF01731581. PMID 7463489. S2CID 19528200.
Hasegawa M, Kishino H, Yano T (October 1985). "Dating of the human-ape splitting by a molecular clock of mitochondrial DNA". Journal of Molecular Evolution. 22 (2): 160–174. Bibcode:1985JMolE..22..160H. doi:10.1007/BF02101694. PMID 3934395. S2CID 25554168.
Kimura M (January 1981). "Estimation of evolutionary distances between homologous nucleotide sequences". Proceedings of the National Academy of Sciences of the United States of America. 78 (1): 454–458. Bibcode:1981PNAS...78..454K. doi:10.1073/pnas.78.1.454. PMC 319072. PMID 6165991.
Tamura K, Nei M (May 1993). "Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees". Molecular Biology and Evolution. 10 (3): 512–526. doi:10.1093/oxfordjournals.molbev.a040023. PMID 8336541.
Zharkikh A (September 1994). "Estimation of evolutionary distances between nucleotide sequences". Journal of Molecular Evolution. 39 (3): 315–329. Bibcode:1994JMolE..39..315Z. doi:10.1007/BF00160155. PMID 7932793. S2CID 33845318.
Huelsenbeck JP, Larget B, Alfaro ME (June 2004). "Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo". Molecular Biology and Evolution. 21 (6): 1123–1133. doi:10.1093/molbev/msh123. PMID 15034130.
Yap VB, Pachter L (April 2004). "Identification of evolutionary hotspots in the rodent genomes". Genome Research. 14 (4): 574–579. doi:10.1101/gr.1967904. PMC 383301. PMID 15059998.
Susko E, Roger AJ (September 2007). "On reduced amino acid alphabets for phylogenetic inference". Molecular Biology and Evolution. 24 (9): 2139–2150. doi:10.1093/molbev/msm144. PMID 17652333.
Arbiza, Leonardo; Patricio, Mateus; Dopazo, Hernán; Posada, David (2011-01-01). "Genome-Wide Heterogeneity of Nucleotide Substitution Model Fit". Genome Biology and Evolution. 3: 896–908. doi:10.1093/gbe/evr080. ISSN 1759-6653. PMC 3175760. PMID 21824869.
Halpern, A. L.; Bruno, W. J. (1998-07-01). "Evolutionary distances for protein-coding sequences: modeling site- specific residue frequencies". Molecular Biology and Evolution. 15 (7): 910–917. doi:10.1093/oxfordjournals.molbev.a025995. ISSN 0737-4038. PMID 9656490.
Gu X, Li WH (September 1992). "Higher rates of amino acid substitution in rodents than in humans". Molecular Phylogenetics and Evolution. 1 (3): 211–214. Bibcode:1992MolPE...1..211G. doi:10.1016/1055-7903(92)90017-B. PMID 1342937.
Li WH, Ellsworth DL, Krushkal J, Chang BH, Hewett-Emmett D (February 1996). "Rates of nucleotide substitution in primates and rodents and the generation-time effect hypothesis". Molecular Phylogenetics and Evolution. 5 (1): 182–187. Bibcode:1996MolPE...5..182L. doi:10.1006/mpev.1996.0012. PMID 8673286.
Martin AP, Palumbi SR (May 1993). "Body size, metabolic rate, generation time, and the molecular clock". Proceedings of the National Academy of Sciences of the United States of America. 90 (9): 4087–4091. Bibcode:1993PNAS...90.4087M. doi:10.1073/pnas.90.9.4087. PMC 46451. PMID 8483925.
Yang Z, Nielsen R (April 1998). "Synonymous and nonsynonymous rate variation in nuclear genes of mammals". Journal of Molecular Evolution. 46 (4): 409–418. Bibcode:1998JMolE..46..409Y. CiteSeerX 10.1.1.19.7744. doi:10.1007/PL00006320. PMID 9541535. S2CID 13917969.
Kishino H, Thorne JL, Bruno WJ (March 2001). "Performance of a divergence time estimation method under a probabilistic model of rate evolution". Molecular Biology and Evolution. 18 (3): 352–361. doi:10.1093/oxfordjournals.molbev.a003811. PMID 11230536.
Thorne JL, Kishino H, Painter IS (December 1998). "Estimating the rate of evolution of the rate of molecular evolution". Molecular Biology and Evolution. 15 (12): 1647–1657. doi:10.1093/oxfordjournals.molbev.a025892. PMID 9866200.
Steel M, Penny D (June 2000). "Parsimony, likelihood, and the role of models in molecular phylogenetics". Molecular Biology and Evolution. 17 (6): 839–850. doi:10.1093/oxfordjournals.molbev.a026364. PMID 10833190.
Bromham L (May 2019). "Six Impossible Things before Breakfast: Assumptions, Models, and Belief in Molecular Dating". Trends in Ecology & Evolution. 34 (5): 474–486. Bibcode:2019TEcoE..34..474B. doi:10.1016/j.tree.2019.01.017. PMID 30904189. S2CID 85496215.
Yang Z, Bielawski JP (December 2000). "Statistical methods for detecting molecular adaptation". Trends in Ecology & Evolution. 15 (12): 496–503. doi:10.1016/s0169-5347(00)01994-7. PMC 7134603. PMID 11114436.
Jermiin, L.S.; Jayaswal, V.; Ababneh, F.; Robinson, J. (2008). "Phylogenetic model evaluation". In Keith, J. (ed.). Bioinformatics: Data, Sequence Analysis, and Evolution. Methods in Molecular Biology. Vol. 1. Totawa: Humana Press. pp. 65–91. doi:10.1007/978-1-60327-159-2_16. ISBN 978-1-58829-707-5. PMID 18566772.
Ponciano JM, Burleigh JG, Braun EL, Taper ML (December 2012). "Assessing parameter identifiability in phylogenetic models using data cloning". Systematic Biology. 61 (6): 955–972. doi:10.1093/sysbio/sys055. PMC 3478565. PMID 22649181.
Whelan S, Goldman N (May 2001). "A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach". Molecular Biology and Evolution. 18 (5): 691–699. doi:10.1093/oxfordjournals.molbev.a003851. PMID 11319253.
Braun EL (July 2018). "An evolutionary model motivated by physicochemical properties of amino acids reveals variation among proteins". Bioinformatics. 34 (13): i350 – i356. doi:10.1093/bioinformatics/bty261. PMC 6022633. PMID 29950007.
Goldman N, Whelan S (November 2002). "A novel use of equilibrium frequencies in models of sequence evolution". Molecular Biology and Evolution. 19 (11): 1821–1831. doi:10.1093/oxfordjournals.molbev.a004007. PMID 12411592.
Kosiol C, Holmes I, Goldman N (July 2007). "An empirical codon model for protein sequence evolution". Molecular Biology and Evolution. 24 (7): 1464–1479. doi:10.1093/molbev/msm064. PMID 17400572.
Tamura K (July 1992). "Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C-content biases". Molecular Biology and Evolution. 9 (4): 678–687. doi:10.1093/oxfordjournals.molbev.a040752. PMID 1630306.
Halpern AL, Bruno WJ (July 1998). "Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies". Molecular Biology and Evolution. 15 (7): 910–917. doi:10.1093/oxfordjournals.molbev.a025995. PMID 9656490. S2CID 7332698.
Braun EL, Kimball RT (August 2002). Kjer K (ed.). "Examining Basal avian divergences with mitochondrial sequences: model complexity, taxon sampling, and sequence length". Systematic Biology. 51 (4): 614–625. doi:10.1080/10635150290102294. PMID 12228003.
Phillips MJ, Delsuc F, Penny D (July 2004). "Genome-scale phylogeny and the detection of systematic biases". Molecular Biology and Evolution. 21 (7): 1455–1458. doi:10.1093/molbev/msh137. PMID 15084674.
Ishikawa SA, Inagaki Y, Hashimoto T (January 2012). "RY-Coding and Non-Homogeneous Models Can Ameliorate the Maximum-Likelihood Inferences From Nucleotide Sequence Data with Parallel Compositional Heterogeneity". Evolutionary Bioinformatics Online. 8 EBO.S9017: 357–371. doi:10.4137/EBO.S9017. PMC 3394461. PMID 22798721.
Simmons MP, Ochoterena H (June 2000). "Gaps as characters in sequence-based phylogenetic analyses". Systematic Biology. 49 (2): 369–381. doi:10.1093/sysbio/49.2.369. PMID 12118412.
Yuri T, Kimball RT, Harshman J, Bowie RC, Braun MJ, Chojnowski JL, et al. (March 2013). "Parsimony and model-based analyses of indels in avian nuclear genes reveal congruent and incongruent phylogenetic signals". Biology. 2 (1): 419–444. doi:10.3390/biology2010419. PMC 4009869. PMID 24832669.
Houde P, Braun EL, Narula N, Minjares U, Mirarab S (2019-07-06). "Phylogenetic Signal of Indels and the Neoavian Radiation". Diversity. 11 (7): 108. Bibcode:2019Diver..11..108H. doi:10.3390/d11070108.
Cavender JA (August 1978). "Taxonomy with confidence". Mathematical Biosciences. 40 (3–4): 271–280. doi:10.1016/0025-5564(78)90089-5.
Farris JS (1973-09-01). "A Probability Model for Inferring Evolutionary Trees". Systematic Biology. 22 (3): 250–256. doi:10.1093/sysbio/22.3.250. ISSN 1063-5157.
Waddell PJ, Penny D, Moore T (August 1997). "Hadamard conjugations and modeling sequence evolution with unequal rates across sites". Molecular Phylogenetics and Evolution. 8 (1): 33–50. Bibcode:1997MolPE...8...33W. doi:10.1006/mpev.1997.0405. PMID 9242594.
Henikoff S, Henikoff JG (November 1992). "Amino acid substitution matrices from protein blocks". Proceedings of the National Academy of Sciences of the United States of America. 89 (22): 10915–10919. Bibcode:1992PNAS...8910915H. doi:10.1073/pnas.89.22.10915. PMC 50453. PMID 1438297.
Altschul SF (March 1993). "A protein alignment scoring system sensitive at all evolutionary distances". Journal of Molecular Evolution. 36 (3): 290–300. Bibcode:1993JMolE..36..290A. doi:10.1007/BF00160485. PMID 8483166. S2CID 22532856.
Kishino H, Miyata T, Hasegawa M (August 1990). "Maximum likelihood inference of protein phylogeny and the origin of chloroplasts". Journal of Molecular Evolution. 31 (2): 151–160. Bibcode:1990JMolE..31..151K. doi:10.1007/BF02109483. S2CID 24650412.
Kosiol C, Goldman N (February 2005). "Different versions of the Dayhoff rate matrix". Molecular Biology and Evolution. 22 (2): 193–199. doi:10.1093/molbev/msi005. PMID 15483331.
Keane TM, Creevey CJ, Pentony MM, Naughton TJ, Mclnerney JO (March 2006). "Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified". BMC Evolutionary Biology. 6 (1) 29. Bibcode:2006BMCEE...6...29K. doi:10.1186/1471-2148-6-29. PMC 1435933. PMID 16563161.
Bigot T, Guglielmini J, Criscuolo A (August 2019). "Simulation data for the estimation of numerical constants for approximating pairwise evolutionary distances between amino acid sequences". Data in Brief. 25 104212. Bibcode:2019DIB....2504212B. doi:10.1016/j.dib.2019.104212. PMC 6699465. PMID 31440543.
Gonnet GH, Cohen MA, Benner SA (June 1992). "Exhaustive matching of the entire protein sequence database". Science. 256 (5062): 1443–1445. Bibcode:1992Sci...256.1443G. doi:10.1126/science.1604319. PMID 1604319.
Jones DT, Taylor WR, Thornton JM (June 1992). "The rapid generation of mutation data matrices from protein sequences". Computer Applications in the Biosciences. 8 (3): 275–282. doi:10.1093/bioinformatics/8.3.275. PMID 1633570.
Le SQ, Gascuel O (July 2008). "An improved general amino acid replacement matrix". Molecular Biology and Evolution. 25 (7): 1307–1320. doi:10.1093/molbev/msn067. PMID 18367465.
Müller T, Vingron M (December 2000). "Modeling amino acid replacement". Journal of Computational Biology. 7 (6): 761–776. doi:10.1089/10665270050514918. PMID 11382360.
Veerassamy S, Smith A, Tillier ER (December 2003). "A transition probability model for amino acid substitutions from blocks". Journal of Computational Biology. 10 (6): 997–1010. doi:10.1089/106652703322756195. PMID 14980022.
Minh, Bui Quang; Dang, Cuong Cao; Vinh, Le Sy; Lanfear, Robert (11 August 2021). "QMaker: Fast and Accurate Method to Estimate Empirical Models of Protein Evolution". Systematic Biology. 70 (5): 1046–1060. doi:10.1093/sysbio/syab010. PMC 8357343. PMID 33616668.
Dang, Cuong Cao; Minh, Bui Quang; McShea, Hanon; Masel, Joanna; James, Jennifer Eleanor; Vinh, Le Sy; Lanfear, Robert (9 February 2022). "nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models". Systematic Biology. 71 (5): 1110–1123. doi:10.1093/sysbio/syac007. PMC 9366462. PMID 35139203.
Iglesias-Rivas, Paula; Del Amparo, Roberto; Cabaleiro, Javier A; Arenas, Miguel (2025-01-18). "Empirical substitution models of protein evolution: database, relationships, and modeling considerations". Database. 2025 baaf052. doi:10.1093/database/baaf052. ISSN 1758-0463. PMC 12462380. PMID 40996708.
Schrempf, Dominik; Lartillot, Nicolas; Szöllősi, Gergely (16 December 2020). "Scalable Empirical Mixture Models That Account for Across-Site Compositional Heterogeneity". Molecular Biology and Evolution. 37 (12): 3616–3631. doi:10.1093/molbev/msaa145. PMC 7743758. PMID 32877529.
Wang, Huai-Chun; Minh, Bui Quang; Susko, Edward; Roger, Andrew J (1 March 2018). "Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation". Systematic Biology. 67 (2): 216–235. doi:10.1093/sysbio/syx068. PMID 28950365.
Tuffley C, Steel M (May 1997). "Links between maximum likelihood and maximum parsimony under a simple model of site substitution". Bulletin of Mathematical Biology. 59 (3): 581–607. doi:10.1007/bf02459467. PMID 9172826. S2CID 189885872.
Holder MT, Lewis PO, Swofford DL (July 2010). "The akaike information criterion will not choose the no common mechanism model". Systematic Biology. 59 (4): 477–485. doi:10.1093/sysbio/syq028. hdl:1808/9209. PMID 20547783. A good model for phylogenetic inference must be rich enough to deal with sources of noise in the data, but ML estimation conducted using models that are clearly overparameterized can lead to drastically wrong conclusions. The NCM model certainly falls in the realm of being too parameter rich to serve as a justification of the use of parsimony based on it being an ML estimator under a general model.
Perron U, Kozlov AM, Stamatakis A, Goldman N, Moal IH (September 2019). Pupko T (ed.). "Modeling Structural Constraints on Protein Evolution via Side-Chain Conformational States". Molecular Biology and Evolution. 36 (9): 2086–2103. doi:10.1093/molbev/msz122. PMC 6736381. PMID 31114882.
Huelsenbeck JP, Hillis DM (1993-09-01). "Success of Phylogenetic Methods in the Four-Taxon Case". Systematic Biology. 42 (3): 247–264. doi:10.1093/sysbio/42.3.247. ISSN 1063-5157.
Goldman N (February 1993). "Statistical tests of models of DNA substitution". Journal of Molecular Evolution. 36 (2): 182–198. Bibcode:1993JMolE..36..182G. doi:10.1007/BF00166252. PMID 7679448. S2CID 29354147.
Church SH, Ryan JF, Dunn CW (November 2015). "Automation and Evaluation of the SOWH Test with SOWHAT". Systematic Biology. 64 (6): 1048–1058. doi:10.1093/sysbio/syv055. PMC 4604836. PMID 26231182.
Lewis PO (2001-11-01). "A likelihood approach to estimating phylogeny from discrete morphological character data". Systematic Biology. 50 (6): 913–925. doi:10.1080/106351501753462876. PMID 12116640.
Lee MS, Cau A, Naish D, Dyke GJ (May 2014). "Morphological clocks in paleontology, and a mid-Cretaceous origin of crown Aves". Systematic Biology. 63 (3): 442–449. doi:10.1093/sysbio/syt110. PMID 24449041.
Ronquist F, Klopfstein S, Vilhelmsen L, Schulmeister S, Murray DL, Rasnitsyn AP (December 2012). "A total-evidence approach to dating with fossils, applied to the early radiation of the hymenoptera". Systematic Biology. 61 (6): 973–999. doi:10.1093/sysbio/sys058. PMC 3478566. PMID 22723471.
Farris JS, Kluge AG, Carpenter JM (June 2001). Olmstead R (ed.). "Popper and likelihood versus "Popper"". Systematic Biology. 50 (3): 438–444. doi:10.1080/10635150119150. PMID 12116585.
Goldman, Nick (December 1990). "Maximum Likelihood Inference of Phylogenetic Trees, with Special Reference to a Poisson Process Model of DNA Substitution and to Parsimony Analyses". Systematic Zoology. 39 (4): 345–361. doi:10.2307/2992355. JSTOR 2992355.
Sun, Haijing; Smith, Martin R.; Zeng, Han; Zhao, Fangchen; Li, Guoxiang; Zhu, Maoyan (26 September 2018). "Hyoliths with pedicles illuminate the origin of the brachiopod body plan". Proceedings of the Royal Society B: Biological Sciences. 285 (1887) 20181780. doi:10.1098/rspb.2018.1780. PMC 6170810. PMID 30257914. Relevant supplemental data page

handle.net (Global: 102^nd place; English: 76^th place)

hdl.handle.net

Holder MT, Lewis PO, Swofford DL (July 2010). "The akaike information criterion will not choose the no common mechanism model". Systematic Biology. 59 (4): 477–485. doi:10.1093/sysbio/syq028. hdl:1808/9209. PMID 20547783. A good model for phylogenetic inference must be rich enough to deal with sources of noise in the data, but ML estimation conducted using models that are clearly overparameterized can lead to drastically wrong conclusions. The NCM model certainly falls in the realm of being too parameter rich to serve as a justification of the use of parsimony based on it being an ML estimator under a general model.

harvard.edu (Global: 18^th place; English: 17^th place)

ui.adsabs.harvard.edu

Yang Z (July 1994). "Estimating the pattern of nucleotide substitution". Journal of Molecular Evolution. 39 (1): 105–111. Bibcode:1994JMolE..39..105Y. doi:10.1007/BF00178256. PMID 8064867. S2CID 15895455.
Felsenstein J (November 1981). "Evolutionary trees from DNA sequences: a maximum likelihood approach". Journal of Molecular Evolution. 17 (6): 368–376. Bibcode:1981JMolE..17..368F. doi:10.1007/BF01734359. PMID 7288891. S2CID 8024924.
Kimura M (December 1980). "A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences". Journal of Molecular Evolution. 16 (2): 111–120. Bibcode:1980JMolE..16..111K. doi:10.1007/BF01731581. PMID 7463489. S2CID 19528200.
Hasegawa M, Kishino H, Yano T (October 1985). "Dating of the human-ape splitting by a molecular clock of mitochondrial DNA". Journal of Molecular Evolution. 22 (2): 160–174. Bibcode:1985JMolE..22..160H. doi:10.1007/BF02101694. PMID 3934395. S2CID 25554168.
Kimura M (January 1981). "Estimation of evolutionary distances between homologous nucleotide sequences". Proceedings of the National Academy of Sciences of the United States of America. 78 (1): 454–458. Bibcode:1981PNAS...78..454K. doi:10.1073/pnas.78.1.454. PMC 319072. PMID 6165991.
Zharkikh A (September 1994). "Estimation of evolutionary distances between nucleotide sequences". Journal of Molecular Evolution. 39 (3): 315–329. Bibcode:1994JMolE..39..315Z. doi:10.1007/BF00160155. PMID 7932793. S2CID 33845318.
Gu X, Li WH (September 1992). "Higher rates of amino acid substitution in rodents than in humans". Molecular Phylogenetics and Evolution. 1 (3): 211–214. Bibcode:1992MolPE...1..211G. doi:10.1016/1055-7903(92)90017-B. PMID 1342937.
Li WH, Ellsworth DL, Krushkal J, Chang BH, Hewett-Emmett D (February 1996). "Rates of nucleotide substitution in primates and rodents and the generation-time effect hypothesis". Molecular Phylogenetics and Evolution. 5 (1): 182–187. Bibcode:1996MolPE...5..182L. doi:10.1006/mpev.1996.0012. PMID 8673286.
Martin AP, Palumbi SR (May 1993). "Body size, metabolic rate, generation time, and the molecular clock". Proceedings of the National Academy of Sciences of the United States of America. 90 (9): 4087–4091. Bibcode:1993PNAS...90.4087M. doi:10.1073/pnas.90.9.4087. PMC 46451. PMID 8483925.
Yang Z, Nielsen R (April 1998). "Synonymous and nonsynonymous rate variation in nuclear genes of mammals". Journal of Molecular Evolution. 46 (4): 409–418. Bibcode:1998JMolE..46..409Y. CiteSeerX 10.1.1.19.7744. doi:10.1007/PL00006320. PMID 9541535. S2CID 13917969.
Bromham L (May 2019). "Six Impossible Things before Breakfast: Assumptions, Models, and Belief in Molecular Dating". Trends in Ecology & Evolution. 34 (5): 474–486. Bibcode:2019TEcoE..34..474B. doi:10.1016/j.tree.2019.01.017. PMID 30904189. S2CID 85496215.
Houde P, Braun EL, Narula N, Minjares U, Mirarab S (2019-07-06). "Phylogenetic Signal of Indels and the Neoavian Radiation". Diversity. 11 (7): 108. Bibcode:2019Diver..11..108H. doi:10.3390/d11070108.
Waddell PJ, Penny D, Moore T (August 1997). "Hadamard conjugations and modeling sequence evolution with unequal rates across sites". Molecular Phylogenetics and Evolution. 8 (1): 33–50. Bibcode:1997MolPE...8...33W. doi:10.1006/mpev.1997.0405. PMID 9242594.
Henikoff S, Henikoff JG (November 1992). "Amino acid substitution matrices from protein blocks". Proceedings of the National Academy of Sciences of the United States of America. 89 (22): 10915–10919. Bibcode:1992PNAS...8910915H. doi:10.1073/pnas.89.22.10915. PMC 50453. PMID 1438297.
Altschul SF (March 1993). "A protein alignment scoring system sensitive at all evolutionary distances". Journal of Molecular Evolution. 36 (3): 290–300. Bibcode:1993JMolE..36..290A. doi:10.1007/BF00160485. PMID 8483166. S2CID 22532856.
Kishino H, Miyata T, Hasegawa M (August 1990). "Maximum likelihood inference of protein phylogeny and the origin of chloroplasts". Journal of Molecular Evolution. 31 (2): 151–160. Bibcode:1990JMolE..31..151K. doi:10.1007/BF02109483. S2CID 24650412.
Keane TM, Creevey CJ, Pentony MM, Naughton TJ, Mclnerney JO (March 2006). "Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified". BMC Evolutionary Biology. 6 (1) 29. Bibcode:2006BMCEE...6...29K. doi:10.1186/1471-2148-6-29. PMC 1435933. PMID 16563161.
Bigot T, Guglielmini J, Criscuolo A (August 2019). "Simulation data for the estimation of numerical constants for approximating pairwise evolutionary distances between amino acid sequences". Data in Brief. 25 104212. Bibcode:2019DIB....2504212B. doi:10.1016/j.dib.2019.104212. PMC 6699465. PMID 31440543.
Gonnet GH, Cohen MA, Benner SA (June 1992). "Exhaustive matching of the entire protein sequence database". Science. 256 (5062): 1443–1445. Bibcode:1992Sci...256.1443G. doi:10.1126/science.1604319. PMID 1604319.
Goldman N (February 1993). "Statistical tests of models of DNA substitution". Journal of Molecular Evolution. 36 (2): 182–198. Bibcode:1993JMolE..36..182G. doi:10.1007/BF00166252. PMID 7679448. S2CID 29354147.

jstor.org (Global: 26^th place; English: 20^th place)

Goldman, Nick (December 1990). "Maximum Likelihood Inference of Phylogenetic Trees, with Special Reference to a Poisson Process Model of DNA Substitution and to Parsimony Analyses". Systematic Zoology. 39 (4): 345–361. doi:10.2307/2992355. JSTOR 2992355.

ms609.github.io (Global: low place; English: low place)

Sun, Haijing; Smith, Martin R.; Zeng, Han; Zhao, Fangchen; Li, Guoxiang; Zhu, Maoyan (26 September 2018). "Hyoliths with pedicles illuminate the origin of the brachiopod body plan". Proceedings of the Royal Society B: Biological Sciences. 285 (1887) 20181780. doi:10.1098/rspb.2018.1780. PMC 6170810. PMID 30257914. Relevant supplemental data page

nih.gov (Global: 4^th place; English: 4^th place)

pubmed.ncbi.nlm.nih.gov

Yang Z (July 1994). "Estimating the pattern of nucleotide substitution". Journal of Molecular Evolution. 39 (1): 105–111. Bibcode:1994JMolE..39..105Y. doi:10.1007/BF00178256. PMID 8064867. S2CID 15895455.
Felsenstein J (November 1981). "Evolutionary trees from DNA sequences: a maximum likelihood approach". Journal of Molecular Evolution. 17 (6): 368–376. Bibcode:1981JMolE..17..368F. doi:10.1007/BF01734359. PMID 7288891. S2CID 8024924.
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Simon, Matt. "Twitter Nerd-Fight Reveals a Long, Bizarre Scientific Feud". Wired.
This article describes the #ParsimonyGate controversy, which provides a concrete example of the debate regarding the philosophical nature of the maximum parsimony criterion. #ParsimonyGate was the reaction on Twitter to an editorial in the journal Cladistics, published by the Willi Hennig Society. The editorial states that the "...epistemological paradigm of this journal is parsimony" and that there are philosophical reasons to prefer parsimony to other methods of phylogenetic inference. Since other methods (i.e., maximum likelihood, Bayesian inference, phylogenetic invariants, and most distance methods) of phylogenetic inference are model-based, this statement implicitly rejects the notion that parsimony is a model.

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Substitution model (English Wikipedia)

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