Geno-Diver is a user-friendly software program designed to simulate complex traits and population structures that resemble livestock species. For more information take a look at the Geno-Diver Website . Some of the modules contained with the software is that you can generate a historical population with a range of linkage dis-equilibrium scenarios, quantitative and/or fitness traits, estimate breeding values using pedigree BLUP, genomic BLUP or marker effects models, optimize matings based on inbreeding and/or breeding values, etc. As time progresses, more modules will be introduced in order to stay in line with the current models and methods used in livestock breeding. Stay Tuned!!!

Program to generate a run-of-homozygosity (ROH) based relationship matrix based relationship matrix. The user provides a minimum length in Megabases that the ROH has to be in order for the program to tag it as a ROH. For example if a ROH is 1.5 Mb long and the cutoff is 2 Mb that ROH will not be utilized to generate a relationship matrix. The concept behind the ROH relationship matrix is that a haplotype that is shared between the parents results in a potential ROH in the progeny, which can occur even if a ROH is not observed in the two parental genomes. Within each chromosome the program, generates one SNP sliding windows. For each window, a ROH relationship matrix is computed as the number of haplotypes that are exactly the same (i.e. result in a ROH) for individuals i and j divided by 2. The minimum and maximum numbers of haplotypes that can be the same is 0 and 4, respectively. The ROHRM for a given window, is essentially the ROH-based version of the classical gametic relationship between a pair of individuals. After calculating all ROHRM across all windows, a genome-wide ROHRM was generated as the average of all ROHRM matrices.

Program that determines whether a region of the genome for an individual is in a ROH of a given length. The user provides a minimum length in Megabases that the ROH has to be in order for the program to tag it as a ROH for an individual. Similar to the ROH Relationship Matrix program, a one sliding window approach is utilized to identify ROH in an individual. The program outputs whether a window is in an ROH and whether a given SNP is contained within a ROH.

Program that identifies haplotypes contained within a run of homozygosity (ROH) associated with reduced performance. A detailed explanation of algorithm is outlined in the paper and is found here. The algorithm comprises 3 steps. Step 1 scans the genome based on marker windows of decreasing size and identifies ROH genotypes associated with an unfavorable phenotype. Within this stage, multiple aggregation steps reduce the haplotype to the smallest possible length. In step 2, the resulting regions are formally tested for significance with the use of a linear mixed model. Lastly, step 3 removes nested windows. The program outputs the associated haplotype that when in an ROH results in an unfavorable haplotype.