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.
If you see mistakes or want to suggest changes, please create an issue on the source repository.
Text and figures are licensed under Creative Commons Attribution CC BY-NC 4.0. Source code is available at https://github.com/sa-book/sa-book.github.io, unless otherwise noted. The figures that have been reused from other sources don't fall under this license and can be recognized by a note in their caption: "Figure from ...".