Software

We are actively involved in development of practical tools to facilitate various aspects of genetic research.

Ian Carr has written a series of applications that can be used as powerful aids to the identification of autozygous regions in high-density SNP data:

AutoSNPa for visual presentation of SNP data and identification of autozygous regions.

IBDfinder for pedigree-independent display of homozygous runs of SNPs.

SNPsetter for harmonization and standardization of SNP data sets.

These programs are all available for download from the links above.

We are also interested in improved methods for rapid mutation analysis:

QSVanalyser quantifies the proportions of allelic or paralogous sequence variants.

GeneScreen is a new program for mutation detection by automated comparison of DNA sequence traces.

Illuminator is a mutation-tolerant alignment and analysis tool for high-throughput mutation detection on the Illumina GA-II clonal sequencing platform.

We have also developed a new program for high-sensitivity DNA melting curve analysis (MCA). Links to these new resources will appear here as they become available.

Smaller utilities:

CofI performs calculation of the parameters R (coefficient of relationship), F (coefficient of inbreeding) and p (probability of autozygosity for a specified allele) for individuals in inbred families of known structure. Cy2T will convert Cyrillic pedigree files to text files usable by CofI.

Illumina2Affy converts Illumina genotype data files to an Affymetrix-style format for use by AutoSNPa, IBDfinder and other programs.

SNPannotator adds back SNP annotation data to Affymetrix SNP6 genotype files, so that they can be used by other analysis programs.