# Alignments

Attention! This functionality has not been fully implemented yet!

In the Alignment representation several sequences can be compared (currently a maximum of two) and insertions, deletions and mismatches are automatically indicated.

In the settings dialog, which can be invoked through "Tools/Alignment" or "Ctrl-G", the sequences to align and the alignment algorithm can be chosen:

- Smit-Waterman for local alignments (e.g., a short sequence to be aligned to a long one)
- Needleman-Wunsch for global alignments (e.g., two sequences of similar length)

For longer sequences, and on slow computers, the alignment algorithm can take several minutes to calculate an alignment!

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