email: I.J.Wilson@ncl.ac.uk
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
> install.packages("packagename.zip",repos=NULL)
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.
Use
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
downloaded.
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).
Micsat | Batwing | Parentage | Hapgen | Ancestors | |
Unix | micsat.tar.gz | batwing.tar.gz | parentage.tar.gz | hapgen.tar.gz | ancestors.tar.gz |
Windows 95/NT | micsat.zip | batwing.exe | parentage.exe | ||
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 |
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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. |
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Parentage
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. download |
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
Last Modified