Table 2.

URL sites useful for the HMDP as well as sites used to develop the HMDP, including sites at The Jackson Laboratory (JAX) (Bar Harbor, ME)

Name	Description	URL
EMMA	Obtain EMMA in an R package	http://mouse.cs.ucla.edu/emma/
EMMA server	Input data and obtain analysis	http://mouse.cs.ucla.edu/emmaserver/
EMMA power simulator	R package allowing statistical power experiment via in silico mapping	http://mouse.cs.ucla.edu/power/
EMMA study design Webserver	Provides power simulations with various background genetic effects and threshold estimations	http://mouse.cs.ucla.edu/emmaserver/powerSimulation/
Mouse HapMap	Latest genetic maps that are regularly updated	http://mouse.cs.ucla.edu/mousehapmap/
Mouse genome informatics (JAX)	Search tools for gene names and chromosomal positions, phenotypes, expression, orthology, and other features	http://www.informatics.jax.org/
SGR HMDP database	Database for HMDP and several F2 studies with cQTL, eQTL, heatmap and correlation analyses	http://systems.genetics.ucla.edu
Genenetwork	Study relationships among phenotypes and genotypes	http://www.genenetwork.org/webqtl/main.py
Mouse phenome database (JAX)	Phenotypes across hundreds of strains contributed by over 200 investigators	http://phenome.jax.org/
Wellcome trust center for human genetics	Center to understand the genetic foundations of human variation and disease	http://www.well.ox.ac.uk/home
Perlegen	Perlegen mouse SNP browser covering 12 classical inbred strains and 4 wild-derived strains	http://mouse.cs.ucla.edu/perlegen/
Mouse genomes project	Nucleotide sequence database for many key mouse strains	http://sanger.ac.uk/resources/mouse/genomes/