Graphical illustration of how TargetVet’s VetHybPiper.sh script estimates paralogy from HybPiper results. First, the assemblies for each target are collated into a single multifasta. These scaffolds are then matched to the reference targets using BLAST. Using the BLAST result, VetTargets_genome.R calculates paralogy % for each target. This process is repeated for each sample in order to populate the paralogy matrix, which DetectParalogs.R analyses to produce summary statistics and visualisations.