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- 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.
- note BIOS viewer
- 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).
- 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
