1. Introduction | 2. Obtaining and installing the MorphoTools2 package | 3. Data import, checking and manipulation | 3.1 Data import | 3.2 Assessing normality of data | 3.2.1 Shapiro-Wilk test of normality | 3.2.2 Histograms | 3.2.3 Normal Q-Q plot | 3.3 Data transformation | 3.4 Box Plots | 3.5 Descriptive statistics | 3.6 Correlations of characters | 3.7 Populations as operational taxonomic units | 3.8 Missing data | 3.8.1 Removing items | 3.8.2 Replacing missing values | 4. Hierarchical clustering | 5. Principal component analysis (PCA) | 6. Principal coordinate analysis (PCoA) | 7. Non-metric multidimensional scaling (NMDS) | 8. Stepwise discriminant analysis | 9. Canonical discriminant analysis (CDA) | Passive prediction of samples. | 10. Classificatory discriminant analysis | 10.1 Linear discriminant analysis (LDA) | 10.2 Quadratic discriminant analysis (QDA) | 10.3 K nearest neighbour classificatory DA | 10.4 Classification of sample individuals based on an independent training set. | Further reading | References