|Newcastle University Home Page with details on publications|
|18 January 2017||JAGS Analysis of Copy Number|
|12 November 2014||Extreme-depth re-sequencing of mitochondrial DNA finds no evidence of paternal transmission in humans Data & Code|
|Inference for Maternal Pedigrees with Partial Selfing IMPPS Home Page|
|QTLtree R library and stand alone program Home Page|
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. 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.
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 Ian.Wilson@ncl.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|
|Web interfaces||Web inferface at BioHP.org|
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.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.
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 18 January 2017