Alignment (pairwise and multiple) is extremely central in biological sequence analysis. Some of the purposes in aligning sequences are:
- Reconstructing Molecular Evolution.
- Matching of Functionally Equivalent Regions.
- Definition of patterns the sequences must contain.
Only alignment of homologous sequences seems meaningful as it is unclear what an alignment of non-homologous sequences means. So as viewed here, an alignment is a partial reconstruction of the path of molecular evolution. This project should teach basic algorithms and programming and introduce the student to a large area of Bioinformatics and Sequence Analysis.