закладки (спрятать)107
- 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).
- A very nice set of references.
- note BIOS viewer
- Where should that paper go?
- Species Distribution Modelling Tools: Tools for processing data associated with species distribution modelling exercises
- converts markdown, latex, html, html5 slides... (not xml)
- has link to pdf
- NIH XML article standard
- by Vince Buffalo
- intro
- structured semantic xml: transfer to other things with stylesheets.
- useful!!!
- big picture talk.
- Note discussion of using EC2 in comments.
- Statistics 110: Introduction to Probability by Joseph Blitzstein Harvard
- The rpanel package has two aims. The first is to provide tools which make the construction of gui control panels for R applications as easy as possible. The package is aimed at those who know R but are not familiar with the technicalities of the various gui construction systems which are available. The rpanel package is built on rtcltk and manages the process of communication so that controls can be constructed directly by R simple function calls.
- The nonlinear equations encyclopedia
- par(oma) and par(mar) explained *graphically*
- can convert PMID to PMCID! pull papers!
- TeXMed is an interface for NCBI PubMed to export and save BibTeX format for import into LaTeX or TeX documents.
- This is Gillespie's most extensive discussion of the use of extreme value theory in the study of molecular evolution.
- 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.
публикации (спрятать)3363
- Probability Theory and Related Fields, 92 (1): 21--39 (1992)
- Probab. Theory Related Fields, 102 (2): 145--158 (1995)
- Proc. Natl. Acad. Sci. U.S.A., (марта 1983)
- Mobile DNA, (1989)
- PLoS Genet, (июня 2009)
- The American Naturalist, 152 (2): 204-224 (1998)
- Genetics, 145 (2): 493-504 (февраля 1997)
- J. Math. Biol., 2 (3): 251--263 (1975)
- The Annals of Applied Probability, 7 (3): 615--647 (1997)
- Ann. Appl. Probab., 20 (1): 1-25 (2010)
- The American Naturalist, 119 (4): 589--595 (1982)
- Annual Review of Genetics, 23 (1): 251-287 (1989)
- Genetics, 178 (4): 2169-2177 (2008)
- Annual Review of Genetics, 36 (1): 389-410 (2002)
- Genome Research, (2009)
- Probability and its Applications (New York) Springer, New York, Second издание, (2008)General theory and structure.
- Science, (2009)
- Science, (2009)
- Baillieres Clin Haematol, 11 (1): 1-51 (марта 1998)
- Stochastic point processes: statistical analysis, theory, and applications (Conf., IBM Res. Center, Yorktown Heights, N.Y., 1971), Wiley-Interscience, New York, (1972)
- Chapman & Hall, London, (1980)Monographs on Applied Probability and Statistics.
- Probability and its Applications (New York) Springer-Verlag, New York, Second издание, (2003)Elementary theory and methods.
- Teor. Verojatnost. i Primenen., (1962)In Russian. Has useful theorem on sum over function of points..
- 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. Appl. Probab., 5 (4): 1008--1024 (1995)
- Comm. Pure Appl. Math., 28 (3): 323--331 (1975)
- Adv. in Math., 30 (1): 33--76 (1978)
- Byul. Moskovskogo Gos. Univ., 1 (6): 1--25 (1937)
- Mat. Sb. (N.S.), 59 (101) (suppl.): 245--288 (1962)
- Genetics, (2009)
- Journal of Statistical Software, 21 (12): 1--20 (15.09.2007)
- Science, (2009)
- Science, 326 (5959): 1546-1549 (2009)
- Science, (2009)
- Genetics, 177 (4): 2083-2099 (2007)
- Genetics Research, 15 (02): 221-225 (1970)
- Evolution, 35 (3): 477--488 (1981)
- Evolution, 59 (1): 216-220 (января 2005)
- École d'été de probabilités de Saint-Flour, XIII---1983, том 1117 из Lecture Notes in Math., Springer, Berlin, (1985)
- Mol Biol Evol, (2006)
- Genetics, 169 (4): 2335-2352 (апреля 2005)
- PLoS Genet, 2 (12): e186 (декабря 2006)
- Ecology, 89 (10): 2700-2711 (2008)
- Proceedings of the IEEE, 70 (9): 939-952 (сентября 1982)
- Advances in Applied Probability, 18 (1): 1--19 (1986)
- 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)
- Journal of the Royal Statistical Society. Series B (Methodological), 39 (3): 283--326 (1977)
- Oxford Studies in Probability The Clarendon Press Oxford University Press, New York, (1993)Oxford Science Publications.
- Probab. Theory Related Fields, 140 (3-4): 319--343 (2008)
- Ecology, 77 (7): 2027--2042 (1996)
- Ensaios Matematicos, 16, cite arxiv:0909.3985 Comment: Lecture notes, to appaear in the collection "Ensaios Matematicos". 17 figures.(2009)
- Nature, 266 (5601): 443--445 (марта 1977)
- Genetics, (октября 2001)
- Advances in Applied Probability, 24 (4): 814--844 (1992)
- Advances in Applied Probability, 27 (2): 367--383 (1995)
- Ann. Math. Statist., (1962)
- Il Nuovo cimento. D, 20 (7-8): 1171--1182 (1998)
- 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..
- Statistics, probability and game theory, том 30 из IMS Lecture Notes Monogr. Ser., Inst. Math. Statist., Hayward, CA, (1996)
- Journal of Applied Probability, (1982)
- Cell, 132 (5): 783--793 (2008)
- Mathematical Biosciences, 206 (1): 81 - 107 (2007)Alcala Special Issue.
- Journal of Theoretical Biology, 244 (3): 424 - 432 (2007)
- Ann. Probab., 37 (4): 1502--1523 (2009)
- The Annals of Probability, 6 (2): 345--348 (1978)
- Proc. London Math. Soc. (3), (1974)Nice reading..
- Genetics, 183 (1): 259-274 (2009)
- Proceedings of the National Academy of Sciences, 106 (38): 16057-16062 (2009)
- PLoS Genet, 3 (11): e185 (ноября 2007)
- Advances in Applied Probability, 14 (2): 359--367 (1982)
- Zeitschrift für Angewandte Mathematik und Physik (ZAMP), 60 (3): 377--392 (мая 2009)
- Nonlinear dynamics and evolution equations, том 48 из Fields Inst. Commun., Amer. Math. Soc., Providence, RI, (2006)
- Journal of Evolution Equations, 8 (1): 189--215 (марта 2008)
- Journal of Dynamics and Differential Equations, 18 (4): 841--861 (октября 2006)
- Nonlinear Analysis: Real World Applications, (2009)
- Nonlinearity, 22 (12): 2813-2844 (2009)
- Systematic Biology, (Number 5/October 2004)
- Journal of Ecology, 82 (4): 933--950 (1994)
- Genetics, (декабря 2002)
- Theoretical Population Biology, 73 (3): 342--348 (2008)
- Mol Biol Evol, 24 (4): 1056-1067 (2007)
- Science, 293 (5529): 455-462 (2001)
- Ann. Hum. Genet., (мая 2007)
- Mol Biol Evol, 24 (3): 710-722 (2007)
- Am. J. Hum. Genet., (января 2008)
- Nat Genet, 39 (1): 31--40 (января 2007)
- Mol Biol Evol, 26 (1): 35-45 (2009)
- Mol. Ecol., (мая 2003)
- PLoS ONE, (2009)
- Science, 313 (5783): 101-104 (2006)
- Proc. Natl. Acad. Sci. U.S.A., (апреля 2003)
- Nat Genet, 38 (1): 107--111 (января 2006)
- PLoS Genet, 5 (1): e1000326 (января 2009)
- Trends in Ecology & Evolution, 23 (1): 26--32 (2008)
- Annual Review of Entomology, 45 (1): 449-466 (2000)
- Adv. in Math., 32 (1): 68--80 (1979)
- Evolution, 13 (4): 568--570 (1959)
- Genetics, 126 (4): 933-948 (1990)
- Nature, 353 (6343): 440--442 (октября 1991)
