Introduction | Installation | Getting Started | Sequence Kernels | Data Representations | Training and Prediction for Binary Classification | Selection of Kernel Parameters, Hyperparameters and Models | Regression | Feature Weights | Prediction Profiles | Multiclass Classification | Definition of Performance Measures for Binary and Multiclass Classification | User-Defined Sequence Kernels | Future Extensions | How to cite this package

Introduction | Installation | msa for the Impatient | Functions for Multiple Sequence Alignment in More Detail | Printing Multiple Sequence Alignments | Processing Multiple Alignments | Pretty-Printing Multiple Sequence Alignments | Known Issues | Future Extensions | How to Cite This Package

Introduction | Installation | Getting Started | Adjusting Input Preferences | Exemplar-based Agglomerative Clustering | Leveraged Affinity Propagation | Sparse Affinity Propagation | Processing Biological Sequences | Similarity Matrices | Miscellaneous | Special Notes for Users Upgrading from Previous Versions | How to Cite This Package

Introduction | Input Data | Predictions Using the Web Interface | Preprocessing Predicted Coiled Coil Segments Using the Web interface | PrOCoil R Package | More Details About PrOCoil | Acknowledgments | How to Cite PrOCoil

Introduction | Installation | PODKAT for the Impatient | Training a Null Model | Selection of Regions of Interest | Performing an Association Test | Analyzing and Visualizing Results | Miscellanea | More Details About PODKAT | Future Extensions | How to Cite This Package

Introduction | Installation | Getting Started | Adjusting Similarities and t-Norms | A Note on Permutation Testing | The Gaussian Rank Correlation Estimator | How to Cite This Package