Chapter 03

Comparing Sequences

TOC Content (click for jumping to examples)
3.1 Dissimilarity measures to compare sequences No code for this section
3.2 Alignment techniques Create example sequences
Optimal matching (OM)
Assigning costs to the alignment operations
3.3 Alignment-based extensions of OM Alternative OM-bases metrics to align sequences
3.4 Nonalignment techniques Alternative metrics to align sequences
3.5 Comparing dissimilarity matrices Correlation for dissimilarity matrices
3.6 Comparing sequences of different length No code for this section
3.7 Beyond the standard full-sample pairwise sequence comparison Alternative options to compare sequences

Chapter 3 introduces techniques to compare whole sequences. After having reviewed the available options, we offer a tool to compare across the dissimilarity matrices that result from the use of different dissimilarity measures. Finally, we discuss a selection of options to compare sequences in the sample to a reference sequence.


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