закладки (спрятать)107
- Looked at 35 RFLPs along a river, saw evidence of unidirectional introgression. Unclear how they picked their loci.
- structured semantic xml: transfer to other things with stylesheets.
- cchar, v. 1.6: Count characters in sequence data. cpg, v. 0.7: Compute the CpG content of DNA sequences. cutSeq, v. 0.11: Cut regions from molecular sequences. generateQuerySbjct, v. 0.4: Generate pairs of homologous DNA sequences. gd, v. 0.12: Calculate genetic diversity (pi, S, and Tajima's D) from aligned DNA sequences with or without sliding window. getSeq, v. 0.4: Get specific sequences from a FASTA file containing multiple entries. ms2dna, v. 1.16: Generate samples of homologous DNA sequences evolved under defined evolutionary scenarios by converting the output of Richard Hudson's coalescent simulation program ms. As of version 1.11, it can also deal with output generated by Gary Chen's fast coalescent simulator MaCS using the pipeline macs [options] | msformatter | ms2dna -a. randomizeSeq, v. 0.8: Randomize sequences. sequencer, v. 1.14: Simulate shotgun sequencing with paired (as of version 1.11) or unpaired reads and a user-defined error rate. simK, v. 0.4: Simulate pair of sequences with given number of substitutions/site (K).
- note BIOS viewer
- The nk model of fitness interactions is examined. This model has been used by previous authors to investigate the effects of fitness epistasis on substitution dynamics in molecular evolution, and to make broader claims about the importance of epistasis. To examine these claims, an infinite-allele approximation is introduced. In this limit, it is shown that the nk model is, at an appropriate level of description, formally identical to the non-epistatic House-of-Cards model—a well-studied model in theoretical population genetics. It is further shown that in many parameter regimes, the analytical results obtained from this infinite-allele approximation are very close to results from the full nk model (with a finite number of alleles per locus). The findings presented shed light on a number of previous results.
- Selection is one of the factors that most influence the shape of genealogical trees. Here we report results of simulations of the infinite-sites version of Moran's model of population genetics aiming at quantifying how the presence of selection affects the branching pattern (topology) of binary genealogical trees. In particular, we consider a scenario of purifying or negative selection in which all mutations are deleterious and each new mutation reduces the fitness of the individual by the same fraction. Analysis of five statistical measures of tree balance or symmetry borrowed from taxonomy indicates that the genealogical trees of samples of populations in which selection is actuating are in the average more asymmetric than neutral trees and that this effect is enhanced by increasing the sample size. However, a quantitative evaluation of the power of these balance measures to detect a tree topology significantly distinct from the neutral one indicates that they are not useful as tests of neutrality of mutations.
- The nonlinear equations encyclopedia
- by Vince Buffalo
публикации (спрятать)3372
- Systematic Biology, (Number 5/October 2004)
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- Science, (2009)
- Ensaios Matematicos, 16, cite arxiv:0909.3985 Comment: Lecture notes, to appaear in the collection "Ensaios Matematicos". 17 figures.(2009)
- Ann. Probab., 37 (4): 1502--1523 (2009)
- Genetics, 183 (1): 259-274 (2009)
- Proceedings of the National Academy of Sciences, 106 (38): 16057-16062 (2009)
- Zeitschrift für Angewandte Mathematik und Physik (ZAMP), 60 (3): 377--392 (мая 2009)
- Nonlinear Analysis: Real World Applications, (2009)
- Nonlinearity, 22 (12): 2813-2844 (2009)
- Mol Biol Evol, 26 (1): 35-45 (2009)
- PLoS ONE, (2009)
- PLoS Genet, 5 (10): e1000686 (октября 2009)
- PLoS Genet, 5 (6): e1000519 (июня 2009)
- PLoS Genet, 5 (1): e1000326 (января 2009)
- Ann. Probab., 37 (2): 615--653 (2009)
- Genetics, 178 (4): 2169-2177 (2008)
- Probability and its Applications (New York) Springer, New York, Second издание, (2008)General theory and structure.
- Ecology, 89 (10): 2700-2711 (2008)
- Probab. Theory Related Fields, 140 (3-4): 319--343 (2008)
- Cell, 132 (5): 783--793 (2008)
- Journal of Evolution Equations, 8 (1): 189--215 (марта 2008)
- Theoretical Population Biology, 73 (3): 342--348 (2008)
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- Journal of Statistical Software, 21 (12): 1--20 (15.09.2007)
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- Mol Biol Evol, 24 (4): 1056-1067 (2007)
- Ann. Hum. Genet., (мая 2007)
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- Nat Genet, 39 (1): 31--40 (января 2007)
- Mol Biol Evol, (2006)
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- Nonlinear dynamics and evolution equations, том 48 из Fields Inst. Commun., Amer. Math. Soc., Providence, RI, (2006)
- Journal of Dynamics and Differential Equations, 18 (4): 841--861 (октября 2006)
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- Probability and its Applications (New York) Springer-Verlag, New York, Second издание, (2003)Elementary theory and methods.
- Annual Review of Genetics, 36 (1): 389-410 (2002)
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- Genetics, (2006)
- Annales de l'Institut Henri Poincare (B) Probability and Statistics, 42 (1): 125--145 (2006)
- Genetics, 169 (4): 2335-2352 (апреля 2005)
- Evolution, 59 (1): 216-220 (января 2005)
- Annales de l'Institut Henri Poincare (B) Probability and Statistics, 40 (1): 53--72 (2004)
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- Mol. Ecol., (мая 2003)
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- Annual Review of Entomology, 45 (1): 449-466 (2000)
- Baillieres Clin Haematol, 11 (1): 1-51 (марта 1998)
- Il Nuovo cimento. D, 20 (7-8): 1171--1182 (1998)
- Ecology, 77 (7): 2027--2042 (1996)
- Statistics, probability and game theory, том 30 из IMS Lecture Notes Monogr. Ser., Inst. Math. Statist., Hayward, CA, (1996)
- Ann. Appl. Probab., 5 (4): 1008--1024 (1995)
- Advances in Applied Probability, 27 (2): 367--383 (1995)
- Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, 349 (1327): 49-59 (1995)
- Journal of Ecology, 82 (4): 933--950 (1994)
- Oxford Studies in Probability The Clarendon Press Oxford University Press, New York, (1993)Oxford Science Publications.
- Advances in Applied Probability, 24 (4): 814--844 (1992)
- Evolution, 46 (2): 412--429 (1992)
- Genetics, 126 (4): 933-948 (1990)
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- Ann. Probab., 17 (2): 444--481 (1989)This paper examines a version of the contact process with a large range. Particles die at rate 1, and a particle is created at an empty site $x$ at rate $łambda$ times the fraction of occupied sites in $y:||x-y||M$. This contact process is dominated by a branching random walk with death rate 1 and birth rate $łambda$, and it is shown that in many ways these two processes are very similar when $M$ is large. In particular, as $M\toınfty$, the critical value for the contact process converges to 1, which is the critical value for branching random walks. The authors obtain precise rates for this convergence, in every dimension, enabling them to describe the ``crossover'' from contact process to branching process behavior in terms of the survival probability of a process started from a single particle. The proofs of the main results use many estimates for branching random walks, further detailing the nature of this crossover behavior..
- Ann. Probab., 16 (3): 1051--1062 (1988)
- Advances in Applied Probability, 18 (1): 1--19 (1986)
- Probability Theory and Related Fields, 73 (4): 481--515 (ноября 1986)
- École d'été de probabilités de Saint-Flour, XIII---1983, том 1117 из Lecture Notes in Math., Springer, Berlin, (1985)
- Proceedings of the IEEE, 70 (9): 939-952 (сентября 1982)
- Journal of Applied Probability, (1982)
- Advances in Applied Probability, 14 (2): 359--367 (1982)
- Evolution, 35 (3): 477--488 (1981)
- Chapman & Hall, London, (1980)Monographs on Applied Probability and Statistics.
- Adv. in Math., 32 (1): 68--80 (1979)
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- The Annals of Probability, 6 (2): 345--348 (1978)
- Journal of the Royal Statistical Society. Series B (Methodological), 39 (3): 283--326 (1977)
- Nature, 266 (5601): 443--445 (марта 1977)
- Comm. Pure Appl. Math., 28 (3): 323--331 (1975)
- Proc. London Math. Soc. (3), (1974)Nice reading..
- Stochastic point processes: statistical analysis, theory, and applications (Conf., IBM Res. Center, Yorktown Heights, N.Y., 1971), Wiley-Interscience, New York, (1972)
- Proceedings of the Sixth Berkeley Symposium on Mathematical Statistics and Probability (Univ. California, Berkeley, Calif., 1970/1971), Vol. III: Probability theory, стр. 579--614. Berkeley, Calif., Univ. California Press, (1972)
- Advances in Applied Probability, 4 (2): 233--257 (1972)
- Genetics Research, 15 (02): 221-225 (1970)
- Teor. Verojatnost. i Primenen., (1962)In Russian. Has useful theorem on sum over function of points..
- Mat. Sb. (N.S.), 59 (101) (suppl.): 245--288 (1962)
- Ann. Math. Statist., (1962)
- Evolution, 13 (4): 568--570 (1959)
- Byul. Moskovskogo Gos. Univ., 1 (6): 1--25 (1937)
- Izv. Akad. Nauk SSSR, Ser. Math, (1937)Computes density of fairly general Johnson-Mehl crystals and the probability that a point is not in a crystal yet..
