Mouse Phylogeny Viewer is a custom genome browser designed by the Center for Genome Dynamics. It provides the user with reliable and detailed answers to questions on the haplotype diversity and phylogenetic origin of the genetic variation underlying any genomic region of most laboratory strains (both classical and wild-derived).

Genome Interval Overlap Calculator is a general purpose application for calculating the interval-by-interval overlap between two input files. One use of this application is to use the output from the MouseIBS tool to "filter out" regions of the genome that are identical between two strains. This could be applied to QTLs, gene lists etc.

TreeQA is a quantitative genome wide association mapping algorithm. TreeQA utilizes local perfect phylogenies constructed in genomic regions exhibiting no evidence of historical recombination. By efficient algorithm design and implementation, TreeQA can efficiently conduct quantitative genome-wide association analysis and is more effective than the previous methods.

This Strain Survey GEM (Gene Expression Miner) holds data for a gene expression survey of 26 inbred mouse strains. Users can perform simple or advanced queries to find various locations of interest (probes, genes, chromosome regions). The data from the probes in these regions can than be downloaded from all 1,236 samples in this experiment or a smaller subset.

The Center for Genome Dynamics Single Nucleotide Polymorphism Database (CGDSNPdb) is a high quality single nucleotide polymorphism (SNP) database with more than 8 Million SNPs from 74 strains of laboratory mice, drawn from several sources.

Imputed Mouse SNP Resource includes full-genome genotype imputations for 88 classical laboratory mouse strains. The tools allow you to filter the full data set down to a particular set of strains and region of interest. You can view the distribution of imputation confidence for the selected strains averaged over your region of interest and then download the filtered data.

Mouse Map Converter is a simple web interface for converting mouse genome coordinates between MIT Markers, base pair positions and centimorgan positions. The conversion process is based on the mouse map described in "A New Standard Genetic Map for the Laboratory Mouse" by Cox et al. 2009.

Center faculty and other researchers have developed online tools for systems level analyses which are not directly funded by the Center.

MouseDivGeno is a R package specifically designed to genotype the Mouse Diversity Genotyping Array, an Affymetrix mouse genotyping array similar to the human SNP 6.0. MouseDivGeno contains functions which allow you to perform genotyping, identify probe sets potentially harboring a new mutation (Variable INtensity Oligonucleotide or VINO, here we call it a vinotyping) and perform CNV analysis.

Downloadable systems genetics software tools developed outside of the Center by Center faculty and other researchers.

SNPtools is a R package that selects SNPs from a set of inbred strains. The software queries the SNP files and quickly returns SNPs for the requested strains in the region of interest. It then allows the user to plot these SNPs, intersect them with genes and classify them.