Introduction | Distance matrix computation | Example 1: Compute k-mer distance matrices for the woodmouse dataset | Example 2: Alignment-free tree-building | Acknowledgements | References

Abstract | Introduction | The 'aphid' package | Hidden Markov Models | Deriving HMMs from sequence data | Profile Hidden Markov Models | File I/O | Sequence Simulation | Model Training | Sequence Alignment | Further Reading | Acknowledgements | References

Introduction | The INSECT learning and classification algorithms | A worked example | Loading the package and data | Classifying sequences | Acknowledgements | References

Abstract | Introduction | The phylogram package | Importing and exporting trees | Example 1: Import and export a tree from a Newick string | Converting tree objects | Example 2: Convert a "phylo" object to a dendrogram | Tree editing/manipulation | Example 3: Building and manipulating dendrograms | Tree visualization | Summary | Acknowledgements | Author Contributions | References