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.
- 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.
- Download the data.
- mailing list
- Looked at 35 RFLPs along a river, saw evidence of unidirectional introgression. Unclear how they picked their loci.
- Evaluates "patterns of introgression across the hybrid zone for 13 diagnostic X-linked loci with known chromosomal positions using a maximum likelihood model". Finds different patterns. Correlates cline width and cline center at different loci.
publications (hide)3385
- Global Ecology and Conservation, (2018)
- Global Ecology and Conservation, (2023)
- Biometrika, 94 (2): 415--426 (2007)
- Ecology, n/a (n/a): e4331 (2024)
- Ecological Applications, 32 (7): e2649 (2022)
