Bioinformatics, Vol 15, 763-764, Copyright © 1999 by Oxford University Press
JM Comeron
SUMMARY: K-Estimator 4.5 is a Windows program that estimates the number of
nucleotide substitutions per site (divergence) when comparing two aligned
nucleotide sequences, both protein-coding and non-coding. Confidence
intervals of the divergence estimates are obtained by Monte Carlo
simulation. AVAILABILITY: The program is available for non-profit use via
anonymous ftp at ftp.bio.indiana. edu/molbio/mswin. CONTACT:
jcomeron@midway.uchicago.edu
ARTICLES
K-Estimator: calculation of the number of nucleotide substitutions per site and the confidence intervals
Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA.
![]()
CiteULike
Connotea
Del.icio.us What's this?
This article has been cited by other articles:
![]() |
Y. Zhao and R. J. Epstein Programmed Genetic Instability: A Tumor-Permissive Mechanism for Maintaining the Evolvability of Higher Species through Methylation-Dependent Mutation of DNA Repair Genes in the Male Germ Line Mol. Biol. Evol., August 1, 2008; 25(8): 1737 - 1749. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. Jorba, R. Campagnoli, L. De, and O. Kew Calibration of Multiple Poliovirus Molecular Clocks Covering an Extended Evolutionary Range J. Virol., May 1, 2008; 82(9): 4429 - 4440. [Abstract] [Full Text] [PDF] |
||||
![]() |
C. Revilla, M. P. Garcillan-Barcia, R. Fernandez-Lopez, N. R. Thomson, M. Sanders, M. Cheung, C. M. Thomas, and F. de la Cruz Different Pathways to Acquiring Resistance Genes Illustrated by the Recent Evolution of IncW Plasmids Antimicrob. Agents Chemother., April 1, 2008; 52(4): 1472 - 1480. [Abstract] [Full Text] [PDF] |
||||
![]() |
E. G. Bakker, M. B. Traw, C. Toomajian, M. Kreitman, and J. Bergelson Low Levels of Polymorphism in Genes That Control the Activation of Defense Response in Arabidopsis thaliana Genetics, April 1, 2008; 178(4): 2031 - 2043. [Abstract] [Full Text] [PDF] |
||||
![]() |
A. Chandra and D. R. Huff Salmacisia, a new genus of Tilletiales: reclassification of Tilletia buchloeana causing induced hermaphroditism in buffalograss. Mycologia, January 1, 2008; 100(1): 81 - 93. [Abstract] [Full Text] [PDF] |
||||
![]() |
C. Casola, D. Hucks, and C. Feschotte Convergent Domestication of pogo-like Transposases into Centromere-Binding Proteins in Fission Yeast and Mammals Mol. Biol. Evol., January 1, 2008; 25(1): 29 - 41. [Abstract] [Full Text] [PDF] |
||||
![]() |
A. G. Koziol and D. G. Durnford Euglena Light-Harvesting Complexes Are Encoded by Multifarious Polyprotein mRNAs that Evolve in Concert Mol. Biol. Evol., January 1, 2008; 25(1): 92 - 100. [Abstract] [Full Text] [PDF] |
||||
![]() |
Z. Hua, X. Meng, and T.-h. Kao Comparison of Petunia inflata S-Locus F-Box Protein (Pi SLF) with Pi SLF Like Proteins Reveals Its Unique Function in S-RNase Based Self-Incompatibility PLANT CELL, November 1, 2007; 19(11): 3593 - 3609. [Abstract] [Full Text] [PDF] |
||||
![]() |
W. Wang, A. V. Perepelov, L. Feng, S. D. Shevelev, Q. Wang, S. N. Senchenkova, W. Han, Y. Li, A. S. Shashkov, Y. A. Knirel, et al. A group of Escherichia coli and Salmonella enterica O antigens sharing a common backbone structure Microbiology, July 1, 2007; 153(7): 2159 - 2167. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. Flowers, E Sezgin, S Kumagai, D. Duvernell, L. Matzkin, P. Schmidt, and W. Eanes Adaptive Evolution of Metabolic Pathways in Drosophila Mol. Biol. Evol., June 1, 2007; 24(6): 1347 - 1354. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. L. Sawyer and H. S. Malik Eukaryotic Transposable Elements and Genome Evolution Special Feature: Positive selection of yeast nonhomologous end-joining genes and a retrotransposon conflict hypothesis PNAS, November 21, 2006; 103(47): 17614 - 17619. [Abstract] [Full Text] [PDF] |
||||
![]() |
W. Ren, W. Li, M. Yu, P. Hao, Y. Zhang, P. Zhou, S. Zhang, G. Zhao, Y. Zhong, S. Wang, et al. Full-length genome sequences of two SARS-like coronaviruses in horseshoe bats and genetic variation analysis. J. Gen. Virol., November 1, 2006; 87(Pt 11): 3355 - 3359. [Abstract] [Full Text] [PDF] |
||||
![]() |
X. Yang, G. A. Tuskan, and Z.-M. Cheng Divergence of the Dof Gene Families in Poplar, Arabidopsis, and Rice Suggests Multiple Modes of Gene Evolution after Duplication Plant Physiology, November 1, 2006; 142(3): 820 - 830. [Abstract] [Full Text] [PDF] |
||||
![]() |
M. L. Federico, F. L. Iniguez-Luy, R. W. Skadsen, and H. F. Kaeppler Spatial and Temporal Divergence of Expression in Duplicated Barley Germin-Like Protein-Encoding Genes Genetics, September 1, 2006; 174(1): 179 - 190. [Abstract] [Full Text] [PDF] |
||||
![]() |
C. J. Ridout, P. Skamnioti, O. Porritt, S. Sacristan, J. D.G. Jones, and J. K.M. Brown Multiple Avirulence Paralogues in Cereal Powdery Mildew Fungi May Contribute to Parasite Fitness and Defeat of Plant Resistance PLANT CELL, September 1, 2006; 18(9): 2402 - 2414. [Abstract] [Full Text] [PDF] |
||||
![]() |
E. G. Bakker, C. Toomajian, M. Kreitman, and J. Bergelson A Genome-Wide Survey of R Gene Polymorphisms in Arabidopsis PLANT CELL, August 1, 2006; 18(8): 1803 - 1818. [Abstract] [Full Text] [PDF] |
||||
![]() |
G. He, X. Luo, F. Tian, K. Li, Z. Zhu, W. Su, X. Qian, Y. Fu, X. Wang, C. Sun, et al. Haplotype variation in structure and expression of a gene cluster associated with a quantitative trait locus for improved yield in rice Genome Res., May 1, 2006; 16(5): 618 - 626. [Abstract] [Full Text] [PDF] |
||||
![]() |
E. Weber and R. Koebnik Positive Selection of the Hrp Pilin HrpE of the Plant Pathogen Xanthomonas J. Bacteriol., February 15, 2006; 188(4): 1405 - 1410. [Abstract] [Full Text] [PDF] |
||||
![]() |
C. E. Vallejos, G. Astua-Monge, V. Jones, T. R. Plyler, N. S. Sakiyama, and S. A. Mackenzie Genetic and Molecular Characterization of the I Locus of Phaseolus vulgaris Genetics, February 1, 2006; 172(2): 1229 - 1242. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. M. Comeron and T. B. Guthrie Intragenic Hill-Robertson Interference Influences Selection Intensity on Synonymous Mutations in Drosophila Mol. Biol. Evol., December 1, 2005; 22(12): 2519 - 2530. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. Heeger, O. Leismann, R. Schittenhelm, O. Schraidt, S. Heidmann, and C. F. Lehner Genetic interactions of separase regulatory subunits reveal the diverged Drosophila Cenp-C homolog Genes & Dev., September 1, 2005; 19(17): 2041 - 2053. [Abstract] [Full Text] [PDF] |
||||
![]() |
A. Llopart, D. Lachaise, and J. A. Coyne Multilocus Analysis of Introgression Between Two Sympatric Sister Species of Drosophila: Drosophila yakuba and D. santomea Genetics, September 1, 2005; 171(1): 197 - 210. [Abstract] [Full Text] [PDF] |
||||
![]() |
Y. Zhang, Y. Wu, Y. Liu, and B. Han Computational Identification of 69 Retroposons in Arabidopsis Plant Physiology, June 1, 2005; 138(2): 935 - 948. [Abstract] [Full Text] [PDF] |
||||
![]() |
A. Narechania, M. Terai, and R. D. Burk Overlapping reading frames in closely related human papillomaviruses result in modular rates of selection within E2 J. Gen. Virol., May 1, 2005; 86(5): 1307 - 1313. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. L. Smits, G. J. Gerwig, A. L. W. van Vliet, A. Lissenberg, P. Briza, J. P. Kamerling, R. Vlasak, and R. J. de Groot Nidovirus Sialate-O-Acetylesterases: EVOLUTION AND SUBSTRATE SPECIFICITY OF CORONAVIRAL AND TOROVIRAL RECEPTOR-DESTROYING ENZYMES J. Biol. Chem., February 25, 2005; 280(8): 6933 - 6941. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. L. Sawyer, L. I. Wu, M. Emerman, and H. S. Malik Positive selection of primate TRIM5{alpha} identifies a critical species-specific retroviral restriction domain PNAS, February 22, 2005; 102(8): 2832 - 2837. [Abstract] [Full Text] [PDF] |
||||
![]() |
L. Liu, T. Wilson, and J. W. Hastings Molecular evolution of dinoflagellate luciferases, enzymes with three catalytic domains in a single polypeptide PNAS, November 23, 2004; 101(47): 16555 - 16560. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. L. Cooper and S. Henikoff Adaptive Evolution of the Histone Fold Domain in Centromeric Histones Mol. Biol. Evol., September 1, 2004; 21(9): 1712 - 1718. [Abstract] [Full Text] [PDF] |
||||
![]() |
D. O. F. Skibinski and R. D. Ward Average Allozyme Heterozygosity in Vertebrates Correlates with Ka/Ks Measured in the Human-Mouse Lineage Mol. Biol. Evol., September 1, 2004; 21(9): 1753 - 1759. [Abstract] [Full Text] [PDF] |
||||
![]() |
R. D'Ovidio, A. Raiola, C. Capodicasa, A. Devoto, D. Pontiggia, S. Roberti, R. Galletti, E. Conti, D. O'Sullivan, and G. De Lorenzo Characterization of the Complex Locus of Bean Encoding Polygalacturonase-Inhibiting Proteins Reveals Subfunctionalization for Defense against Fungi and Insects Plant Physiology, August 1, 2004; 135(4): 2424 - 2435. [Abstract] [Full Text] [PDF] |
||||
![]() |
D. Lindell, M. B. Sullivan, Z. I. Johnson, A. C. Tolonen, F. Rohwer, and S. W. Chisholm Transfer of photosynthesis genes to and from Prochlorococcus viruses PNAS, July 27, 2004; 101(30): 11013 - 11018. [Abstract] [Full Text] [PDF] |
||||
![]() |
M. Hasselmann and M. Beye Signatures of selection among sex-determining alleles of the honey bee PNAS, April 6, 2004; 101(14): 4888 - 4893. [Abstract] [Full Text] [PDF] |
||||
![]() |
A. Fiebig, R. Kimport, and D. Preuss Comparisons of pollen coat genes across Brassicaceae species reveal rapid evolution by repeat expansion and diversification PNAS, March 2, 2004; 101(9): 3286 - 3291. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. R. Reichman, T. P. Wilcox, and P. D. Vize PCP Gene Family in Symbiodinium from Hippopus hippopus: Low Levels of Concerted Evolution, Isoform Diversity, and Spectral Tuning of Chromophores Mol. Biol. Evol., December 1, 2003; 20(12): 2143 - 2154. [Abstract] [Full Text] [PDF] |
||||
![]() |
L. A. Sheldahl, D. M. Weinreich, and D. M. Rand Recombination, Dominance and Selection on Amino Acid Polymorphism in the Drosophila Genome: Contrasting Patterns on the X and Fourth Chromosomes Genetics, November 1, 2003; 165(3): 1195 - 1208. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. L. Smits, A. Lavazza, K. Matiz, M. C. Horzinek, M. P. Koopmans, and R. J. de Groot Phylogenetic and Evolutionary Relationships among Torovirus Field Variants: Evidence for Multiple Intertypic Recombination Events J. Virol., September 1, 2003; 77(17): 9567 - 9577. [Abstract] [Full Text] [PDF] |
||||
![]() |
T. Gubitz, A. Caldwell, and A. Hudson Rapid Molecular Evolution of CYCLOIDEA-like Genes in Antirrhinum and Its Relatives Mol. Biol. Evol., September 1, 2003; 20(9): 1537 - 1544. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. Shi, H. Xi, Y. Wang, C. Zhang, Z. Jiang, K. Zhang, Y. Shen, L. Jin, K. Zhang, W. Yuan, et al. Divergence of the genes on human chromosome 21 between human and other hominoids and variation of substitution rates among transcription units PNAS, July 8, 2003; 100(14): 8331 - 8336. [Abstract] [Full Text] [PDF] |
||||
![]() |
E. Y. Xu, D. F. Lee, A. Klebes, P. J. Turek, T. B. Kornberg, and R. A. Reijo Pera Human BOULE gene rescues meiotic defects in infertile flies Hum. Mol. Genet., January 15, 2003; 12(2): 169 - 175. [Abstract] [Full Text] [PDF] |
||||
![]() |
E. Betran, K. Thornton, and M. Long Retroposed New Genes Out of the X in Drosophila Genome Res., December 1, 2002; 12(12): 1854 - 1859. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. I. Wright, B. Lauga, and D. Charlesworth Rates and Patterns of Molecular Evolution in Inbred and Outbred Arabidopsis Mol. Biol. Evol., September 1, 2002; 19(9): 1407 - 1420. [Abstract] [Full Text] [PDF] |
||||
![]() |
C. Toomajian and M. Kreitman Sequence Variation and Haplotype Structure at the Human HFE Locus Genetics, August 1, 2002; 161(4): 1609 - 1623. [Abstract] [Full Text] [PDF] |
||||
![]() |
P. B. Talbert, R. Masuelli, A. P. Tyagi, L. Comai, and S. Henikoff Centromeric Localization and Adaptive Evolution of an Arabidopsis Histone H3 Variant PLANT CELL, May 1, 2002; 14(5): 1053 - 1066. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. N. Avedisov, I. B. Rogozin, E. V. Koonin, and B. J. Thomas Rapid Evolution of a Cyclin A Inhibitor Gene, roughex, in Drosophila Mol. Biol. Evol., November 1, 2001; 18(11): 2110 - 2118. [Abstract] [Full Text] [PDF] |
||||
![]() |
M. A. Jensen, H. L. True, Y. O. Chernoff, and S. Lindquist Molecular Population Genetics and Evolution of a Prion-like Protein in Saccharomyces cerevisiae Genetics, October 1, 2001; 159(2): 527 - 535. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. Yi and B. Charlesworth A Selective Sweep Associated With a Recent Gene Transposition in Drosophila miranda Genetics, December 1, 2000; 156(4): 1753 - 1763. [Abstract] [Full Text] |
||||
![]() |
J. M. Comeron and M. Kreitman The Correlation Between Intron Length and Recombination in Drosophila: Dynamic Equilibrium Between Mutational and Selective Forces Genetics, November 1, 2000; 156(3): 1175 - 1190. [Abstract] [Full Text] |
||||
![]() |
A. Llopart and M. Aguadé Nucleotide Polymorphism at the RpII215 Gene in Drosophila subobscura: Weak Selection on Synonymous Mutations Genetics, July 1, 2000; 155(3): 1245 - 1252. [Abstract] [Full Text] |
||||














