|Newcastle University Home Page with details on publications|
|Additional Material for Vickers, McLeod, Spector & Wilson (2001) BLOOD|
Packages (with varying degree of completeness) for the R software system. Latest versions
in my R package directory
Install packages on unix/linux using the commands
R CMD INSTALL packagename.tar.gz
To install on a windows systems use the zip versions
and install from within R using
Where you have downloaded the package to your working directory. Once installed the zip file can be safely deleted.
|genealogy.tar.gz||genealogy.zip||A package for the simulation of simple population genetic models|
|genomic.tar.gz||genomic.zip||A package for downloading and using HAPMAP and Perlegen datasets|
|pac.tar.gz||pac.zip||A package using Li & Stephens (2003) model for the analysis of genetic data, and my extensions for the analysis of data from subdivided populations.|
|ARG.tar.gz||ARG.zip||Simulate and extract information from Ancestral Recombination Graphs|
|batwing.tar.gz||batwing.zip||Package for postprocessing of BATWING output.|
Screenshots of interactive plots from the ARG package. Left plot shows a view of an ancestral graph showing genetic variants (bottom panel) along with the tree under a single site (top left panel) and tree heights and lengths (top right panel). Right plot gives views of trees 100 sites apart. Click on either plot for a larger view.
All Software on this page is in the form of zipped tar files.
gunzip -c filename.tar.gz | tar xf -
then type make
to compile the program. A limited manual for micsat is in the file micsat.doc. Other manuals can be downloaded in pdf format.
The programs are distributed as executable files in a zip file format
A binhex-ed executable for the Macintosh, MacBatwing, may be
On launching, the program opens a dialog box with a text field. The user puts the program arguments (infile outfile seed) into this field and hits ok.
(Compilation on the Mac courtesy of Oliver Pybus - send comments/bugs to I.Wilson@maths.abdn.ac.uk).
|Macintosh (MacOS 8.0 or above)||MacBatwing|
|Manuals (pdf format)||bat_guide.pdf||parentage.pdf|
|Examples (inc R code)||parexamples.tar.gz|
|Postprocessing (S/R code)||batwing.r|
This is the program described in the paper "Genealogical inference from microsatellite data" by Wilson and Balding published in Genetics 150: 499-510.
A description of the program and the downloaded files.
Bayesian Analysis of Trees With Internal Node Generation. Batwing is described in
Wilson, Weale & Balding 2003.Inferences from DNA data:
population histories, evolutionary processes and forensic match
probabilities. Journal of the Royal Statistical Society: Series
A, 166: 155-188.
Program described in Emery, Wilson, Craig, Boyle and Noble (2001). Assignment of paternity groups without access to parental genotypes: multiple mating and development plasticity in squid. Molecular Ecology: 10: 1265-1278.
A program for haplotype reconstruction from genotypes. Work done with David Cooper.
This program is a Markov chain Monte Carlo method to reconstruct haplotypes from genotypes. It uses Metropolis coupled chains to speed up mixing.
Includes options to deal with:
analysis of Twins Multivariate Normal Model, and Twins Stem Cell Number