Here's the PDF of the poster I presented at the CSH Rat Genome meeting earlier in December. It includes an overview of the user interface and what each option can be used for, along with some example analyses:

1. Gimap region of RNO4 showing identification of informative SNPs between a group of strains.
2. Analysis of LEXF x FXLE recombinant inbred lines in the region of a Cholesterol level QTL on RNO5
3. Hypertensive vs Normotensive strains across a region of RNO5 associated with many hypertension QTL.

I've just finished an enhancement to the SNPlotyper tool that connects the application up to the R statistical package so it can use hierarchical clustering to order the strains. This means that you can define a region, select the strains you wish to analyze and then use the clustering option to group the strains based on similar genotype across the region. You can still manually order the strains as before by using the drag and drop feature on the main SNPlotyper form.

I have updated the SNPlotyper tool (http://snplotyper.mcw.edu) with the full STAR SNP and genotype data. There were a few related bug fixes and interface improvements that went along with it too but now we have all 20,000+ SNPs and their genotypes in over 300 strains in the tool and able to be used.

Please feel free to give the tool a try and let me know how it goes. Any thoughts for improvements to the interface or other suggestions for the analyses would be most appreciated.

Simon.