TaxI2

Calculates genetic differences between DNA sequences

Scores for alignment

The file data/scores.tab contains the scores used in the sequence alignment. Each line has the format:

score_identifier<Tab>value

The possible scores are:

• gap penalty: Score to open a gap in the middle of a sequence
• gap extend penalty: Score to extend an existing gap in the middle of a sequence
• end gap penalty: Score to create a gap at an end of a sequence.
• end gap extend penalty: Score to extend a gap at an end of a sequence.
• match score: Score for matching nucleotides
• mismatch score: Score for non-matching nucleotides