bookmarks (hide)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.
publications (hide)3378
- Toxicon, 60 (6): 1057-1062 (2012)
- Toxicon, (2022)
- Current Biology, 26 (12): 1616-1621 (2016)
- BioScience, 49 (7): 557-568 (July 1999)
- (February 2024)
- Proceedings of the National Academy of Sciences, 56 (3): 864-871 (1966)
- PLoS Biology, 6 (3): e60 (March 2008)
- Proceedings of the Royal Society B: Biological Sciences, 277 (1698): 3317--3325 (November 2010)
- Nature, 434 (7034): 759--763 (April 2005)
- Evolution, 71 (6): 1504-1518 (2017)
- Evolution, 53 (2): 626-631 (1999)
- Molecular Biology and Evolution, 31 (11): 2836-2846 (August 2014)
- Proceedings of the National Academy of Sciences, 109 (12): 4556--4561 (March 2012)
- Functional Ecology, 37 (8): 2170-2180 (2023)
- Journal of Chemical Ecology, (Jun 6, 2024)
- (2024)
- Ecography, 40 (7): 817-828 (2017)
- Genetics, (May 2024)
- Proceedings of the National Academy of Sciences of the United States of America, 85 (17): 6414--6418 (September 1988)
- Nature Reviews Genetics, 14 (4): 262--274 (Apr 1, 2013)
- Nature, 267 (5608): 275--276 (May 1977)
- PLoS genetics, 4 (12): e1000304--e1000304 (December 2008)
- Ecology, 41 (3): 494--508 (1960)
- Cambridge University Press, Cambridge, (2004)
- bioRxiv, (2024)
- Genetics, 224 (2): iyad068 (April 2023)
- Proceedings of the National Academy of Sciences, 102 (44): 15942-15947 (2005)
- Genetics, 215 (1): 193-214 (May 2020)
- Genetics, 221 (1): iyac044 (2022)
- Theoretical population biology, (October 2021)
- Genetics, 51 (3): 411--424 (March 1965)
- Theoretical Population Biology, 5 (2): 257-283 (1974)
- Nature Communications, 5 (1): 5770 (Dec 23, 2014)
- Bioinformatics (Oxford, England), 34 (13): i187--i194 (July 2018)
- Princeton University Press, (1982)
- Methods in Ecology and Evolution, 10 (7): 1072-1082 (2019)
- Ecological Applications, 27 (3): 916-924 (2017)
- Biological Conservation, (2018)
- Ecology, 103 (10): e3473 (2022)
- Proceedings of the National Academy of Sciences, 117 (48): 30531-30538 (2020)
- Ecological Monographs, 89 (3): e01364 (2019)
- Ecology, 100 (6): e02715 (2019)
- Methods in Ecology and Evolution, 5 (12): 1351-1360 (2014)
- PLOS Genetics, 20 (1): 1-24 (January 2024)
- Oxford University Press, (April 2003)
- bioRxiv, (2024)
- Sinauer Sunderland, MA, (2000)
- The American Naturalist, 181 (4): 506-519 (2013)
- Journal of Mathematical Biology, 79 (1): 393--431 (Jul 1, 2019)
- Journal of Animal Ecology, 75 (4): 837-851 (2006)
