Research Page for Ian Wilson

Institute of Biosciences
Newcastle University

ian.wilson@newcastle.ac.uk
Institutional Home Page with contact details and publications

This page contains links to example code, code fragments and source code that are used in published and ongoing work.

My other staff website. This is driven by Newcastle University's WordPress server.

May 2017	Diversit-tag. Code for the paper Abundant and equipotent founder cells establish and maintain acute lymphoblastic leukaemia by A Elder, S Bomken, I Wilson et al.. Leukemia volume 31: 2577–2586 is on github at github.com/ijwilson/diversit-tag.
January 2017	JAGS Analysis of Copy Number A Second document Estimating Copy Number Frequencies from Censored Genotype Data looks at the differences between inference with all genotypes and for censored data.
January 2016	Mitochondrial DNA sequence characteristics modulate the size of the genetic bottleneck 2016. Wilson et al. Hum. Mol. Genet. 25 (5): 1031-1041. Code on github
November 2014	Extreme-depth re-sequencing of mitochondrial DNA finds no evidence of paternal transmission in humans. Pyle et al. 2015. PloS Genetics. Data & Code
	A Markov chain Monte Carlo strategy for sampling from the joint posterior distribution of pedigrees and population parameters under a Fisher–Wright model with partial selfing. 2007. Theor. Popul. Biol. The program described in this paper is Inference for Maternal Pedigrees with Partial Selfing IMPPS Home Page
	QTLtree R library and stand alone program Home Page
	Titin founder mutation is a common cause of myofibrillar myopathy with early respiratory failure. 2014. Pfeffer et al. Code and data Shared Haplotypes.

Public Github repositories

Shiny Population Genetics

Shiny applications for teaching population genetics

Bottleneck Selection: Selection through a bottleneck
SnakeDrift: Simple Pictoral representation of Genetic Drift
SelectionDriftSimulation: Simulation of Drift and Selection

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. link

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 in this section 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 Ian.Wilson@ncl.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)	micsat	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

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.
Download

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:

Known phase,
Missing Data,
Multiple subpopulations

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

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

ian.wilson@newcastle.ac.uk

Last Modified 27 January 2017

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. link