Introduction | Data Objects | What This Vignette Covers | 1. General Setup | 2. Peak Scoring | Batch Import and Extracting .fsa Data | Match Sizing Ladder | Scoring Peaks by Marker | Combining, Cleaning, and Exporting the Peak Dataframe | 3. Data Manipulation | Initial Data Manipulation | Replicate Check | Data Manipulation for Genetic Analysis | OPTIONAL Binding Markers and Exporting Allele Frequencies | 4. Genetic Analysis | Loading the Dataset | Calculating Gene Identity and Genetic Distance Matrices | 1. Counting loci successfully genotyped for each individual (TypedLoci). | 2. Calculating pairwise gene identity for all samples (GeneIdentityMatrix). | 3. Deriving a genetic distance matrix (GeneticDistanceMatrix). | Differentiation Indices | PCA Plot | Phylogenetic Tree | Conclusion