DOI: 10.1007/bf00160154. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods

Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods

10.1007/bf00160154

Crossref journal-article

Springer Science and Business Media LLC

Journal of Molecular Evolution (297)

Bibliography

Yang, Z. (1994). Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods. Journal of Molecular Evolution, 39(3), 306â314.

Authors 1

Ziheng Yang (first)

References 29 Referenced 2,360

Best DJ, Roberts DE (1975) The percentage points of the ?2 distribution. Appl Statist 24:385?388 (10.2307/2347113) / Appl Statist by DJ Best (1975)
Bhattacharjee GP (1970) The incomplete gamma integral. Appl Statist 19:285?287 (10.2307/2346339) / Appl Statist by GP Bhattacharjee (1970)
Brown WM, Prager EM, Wang A, Wilson AC (1982) Mitochondrial DNA sequences of primates, tempo and mode of evolution. J Mol Evol 18:225?239 (10.1007/BF01734101) / J Mol Evol by WM Brown (1982)
Cavalli-Sforza LL, Edwards AWF (1967) Phylogenetic analysis: models and estimation procedures. Evolution 32:550?570 (10.1111/j.1558-5646.1967.tb03411.x) / Evolution by LL Cavalli-Sforza (1967)
Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368?376 (10.1007/BF01734359) / J Mol Evol by J Felsenstein (1981)
Fitch WM (1986) The estimate of total nucleotide substitutions from pairwise differences is biased. Philos Trans R Soc Lond Biol 312: 317?324 (10.1098/rstb.1986.0010) / Philos Trans R Soc Lond Biol by WM Fitch (1986)
Fitch WM, Margolish E (1967) A method for estimating the number of invariant amino acid coding positions in a gene, using cytochrome c as a model case. Biochem Genet 1:65?71 (10.1007/BF00487738) / Biochem Genet by WM Fitch (1967)
Fitch WM, Markowitz E (1970) An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution. Biochem Genet 4:579?593 (10.1007/BF00486096) / Biochem Genet by WM Fitch (1970)
Goldman N (1993) Statistical tests of models of DNA substitution. J Mol Evol 36:182?198 (10.1007/BF00166252) / J Mol Evol by N Goldman (1993)
Hasegawa M (1991) Molecular phylogeny and man's place in Hominoidea. J Anthrop Soc Nippon 99:49?61 (10.1537/ase1911.99.49) / J Anthrop Soc Nippon by M Hasegawa (1991)
Hasegawa M, Horai J (1991) Time of the deepest root for polymorphism in human mitochondrial DNA. J Mol Evol 32:37?42 (10.1007/BF02099927) / J Mol Evol by M Hasegawa (1991)
Hasegawa M, Kishino H (1989) Confidence limits on the maximum likelihood estimation of the hominoid tree from mitochondrial DNA sequences. Evolution 43:672?677 / Evolution by M Hasegawa (1989)
Hasegawa M, Kishino H, Yano T (1985) Dating the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22: 160?174 (10.1007/BF02101694) / J Mol Evol by M Hasegawa (1985)
Hasegawa M, Rienzo AD, Kocher TD, Wilson AC (1993) Toward a more accurate time scale for the human mitochondrial DNA tree. J Mol Evol 37:347?354 (10.1007/BF00178865) / J Mol Evol by M Hasegawa (1993)
Holmquist R, Goodman M, Conry T, Czelusniak I (1983) The spatial distribution of fixed mutations within genes coding for proteins. J Mol Evol 19:137?448 (10.1007/BF02300751) / J Mol Evol by R Holmquist (1983)
Jin L, Nei M (1990) Limitations of the evolutionary parsimony method of phylogeny analysis. Mol Biol Evol 7:82?102 / Mol Biol Evol by L Jin (1990)
Kocher TD, Wilson AC (1991) Sequence evolution of mitochondrial DNA in humans and chimpanzees: Control region and a protein-coding region. In: Osawa S, Honjo T (eds) Evolution of life: fossils, molecules, and culture. Springer-Verlag, Tokyo, pp 391?413 (10.1007/978-4-431-68302-5_25) / Evolution of life: fossils, molecules, and culture by TD Kocher (1991)
Li W-H, Gouy M, Sharp PM, O'hUigin C, Yang Y-W (1990) Molecular phylogeny of rodentia, lagomorpha, primates, artiodactyla, and carnivora and molecular clocks. Proc Natl Acad Sci USA 87: 6703?6707 (10.1073/pnas.87.17.6703) / Proc Natl Acad Sci USA by W-H Li (1990)
Navidi WC, Churchill GA, von Haeseler A (1991) Methods for inferring phylogenies from nucleotide acid sequence data by using maximum likelihood and linear invariants. Mol Biol Evol 8:128?143 / Mol Biol Evol by WC Navidi (1991)
Nei M, Gojobori T (1986) Simple methods for estimating the number of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3:418?426 / Mol Biol Evol by M Nei (1986)
Palumbi SR (1989) Rates of molecular evolution and the function of nucleotide positions free to vary. J Mol Evol 29:180?187 (10.1007/BF02100116) / J Mol Evol by SR Palumbi (1989)
Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512?526 / Mol Biol Evol by K Tamura (1993)
Thorne JL, Kishino H, Felsenstein J (1992) Inching toward reliability: an improved likelihood model of sequence evolution. J Mol Evol 34:3?16 (10.1007/BF00163848) / J Mol Evol by JL Thorne (1992)
Uzzell T, Corbin KW (1971) Fitting discrete probability distributions to evolutionary events. Science 172:1089?1096 (10.1126/science.172.3988.1089) / Science by T Uzzell (1971)
Wakeley J (1993) Substitution rate variation among sites in hypervariable region 1 of human mitochondrial DNA. J Mol Evol 37:613?623 (10.1007/BF00182747) / J Mol Evol by J Wakeley (1993)
Yang Z (1993) Maximum likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol Biol Evol 10:1396?1401 / Mol Biol Evol by Z Yang (1993)
Yang Z (in press) Estimating the pattern of nucleotide substitution. J Mol Evol (10.1007/BF00178256)
Yang Z, Wang T (in press) Mixed model analysis of DNA sequence evolution. Biometrics (10.2307/2532943)
Yang Z, Goldman N, Friday AE (1994) Comparison of models for nucleotide substitution used in maximum likelihood phylogenetic estimation. Mol Biol Evol 11:316?324 / Mol Biol Evol by Z Yang (1994)

Dates

Type	When
Created	20 years, 10 months ago (Nov. 2, 2004, 4:48 a.m.)
Deposited	6 years, 4 months ago (April 8, 2019, 8:26 a.m.)
Indexed	5 hours, 50 minutes ago (Sept. 4, 2025, 9:27 a.m.)
Issued	31 years ago (Sept. 1, 1994)
Published	31 years ago (Sept. 1, 1994)
Published Print	31 years ago (Sept. 1, 1994)

Funders 0

None

BibTeX

@article{Yang_1994, title={Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods}, volume={39}, ISSN={1432-1432}, url={http://dx.doi.org/10.1007/bf00160154}, DOI={10.1007/bf00160154}, number={3}, journal={Journal of Molecular Evolution}, publisher={Springer Science and Business Media LLC}, author={Yang, Ziheng}, year={1994}, month=sep, pages={306–314} }

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