Home Page for Ian Wilson

email: Ian.Wilson@ncl.ac.uk

Newcastle University Home Page with details on publications
Additional Material for Vickers, McLeod, Spector & Wilson (2001) BLOOD
Inference for Maternal Pedigrees with Partial Selfing IMPPS Home Page
QTLtree R library and stand alone program Home Page

R packages

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. Requires the ape package for plots.
batwing.tar.gz batwing.zip Package for postprocessing of BATWING output.
ijwtools.tar.gz ijwtools.zip My own set of utility functions (mainly for dealing with genetic data and the results from my own programs) including quick reading from xml files, omnibus tests, Manhattan distances between rows in a table, multivariate D' calculation.
snptree Create and plot lexical trees from SNP data. Used in paper Recent mitochondrial DNA mutations increase the risk of developing multiple common late-onset human diseases, by Hudson et al.

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.

C/C++ Software

Unix Systems

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.

Windows (95/98/NT)

The programs are distributed as executable files in a zip file format

Macintosh (MacOS 8.0 or above)

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      
Web interfaces     Web inferface at BioHP.org     



Program Descriptions

Micsat

Micsat logo

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.

BATWING logo

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.
Download

Parentage logo 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

The Computational Biology Service Unit at Cornell University provides free world-wide access to parentage via a web interface (BioHPC.org). Using this interface, researchers can run a variety of computationally intensive bioinformatics and population genetics tools, Parentage being one of them.

Web inferface at BioHP.org


Hapgen

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:


Ancestors

Inference of migration or population splitting using importance sampling.

Additional Material

Vickers, McLeod, Spector & Wilson (2001). Assessment of mechanism of skewed X-inactivation by analysis of twins. BLOOD: 97: 1274-1281

BUGS analysis of Twins Multivariate Normal Model, and Twins Stem Cell Number


I.J.Wilson@ncl.ac.uk

Last Modified 19 March 2014