Haplotype-based scans to detect natural selection are useful to identify recent or ongoing positive selection in genomes. Selscan is an efficient multithreaded application that implements Extended Haplotype Homozygosity (EHH), Integrated Haplotype Score (iHS), and Cross-population EHH (XPEHH). Selscan was published in Molecular Biology and Evolution at 2014 by Zachary et al. (https://doi.org/10.1093/molbev/msu211).

A tool for Selscan selection analysis using dog10K project data is provided here. The data we used here (https://kiddlabshare.med.umich.edu/dog10K/phased-imputation-panel/) was after filtered (https://doi.org/10.1186/s13059-023-03023-7), which included 1929 individuals.

You can first select the analysis method you wish to use in the ‘Method’ section (XP-nsl, XP-EHH, iHS, iHH12 and nSL), then select the ssamples to be analysed in the 'Group' box below and add them to the ‘Selected’ box on the right, you can use keyword search to filter samples of a particular category (note case sensitivity). Finally, enter the email address and click 'Submit'. The Selscan selection analysis of the relevant group will be run on our server. Due to the long running time (several hours to several days), the final result will be sent to you by email.

To calculate iHS:selscan --ihs --vcf  --map  --out 
To calculate nSL:selscan --nsl --vcf  --out 
To calculate XP-nSL:selscan --xpnsl --vcf  --vcf-ref  --out 
To calculate iHH12:selscan --ihh12 --vcf  --map  --out 
To calculate XP-EHH:selscan --xpehh --vcf  --vcf-ref  --map  --out