Mouse Genetics and Genomics Software and Tools


We have developed several tools for the analysis of mouse genetics and genomics datasets. Thee tools and the webservers which display the results of analysis with these tools are available to the scientific community.

Mouse Resources:

About the Mouse HapMap

The Mouse HapMap aims to create a genome-wide haplotype map in all commonly used inbred lab strains of mice in order to enable efficient positional cloning and genotype-phenotype correlation studies. Recent data has established that the genomes of commonly used inbred lab mice, the primary mammalian model system, are simple mosaics of long segments from a limited number of distinct subspecies of Mus musculus. By providing a more complete catalog of variation patterns in each modern strain and their origins, the map will allow the use of QTL mapping data from many crosses simultaneously, as well as strain phenotype data, to accelerate the fine mapping and identification of genes responsible for medically relevant phenotypes.

About the NIEHS/Perlegen Mouse Resequencing Data

The National Institute of Environmental Health Sciences (NIEHS) contracted with Perlegen Sciences, Inc. to identify DNA polymorphisms (SNPs) in 15 commonly used strains of inbred laboratory mice (N01-ES-45530). Using high-density oligonuclueotide array technology, the study identified over 8 million SNPs and other genetic differences between these strains and the previously sequenced C57BL/6J reference strains (Phase 1). By leveraging data provided by Mark Daly's research team at the Broad Institute, genotypes were also predicted for 40 other common strains (Phase 2).