CLC Genomics Workbench has two algorithms for calculating alignments:
- Fast (less accurate). This allows for use of an optimized alignment algorithm which is very fast. The fast option is particularly useful for data sets with very long sequences.
- Slow (very accurate). This is the recommended choice unless you find the processing time too long.
Both algorithms use progressive alignment. The faster algorithm builds the initial tree by doing more approximate pairwise alignments than the slower option.