Example Gap Squeeze

Goal: You want to remove only those columns from your alignment that are entirely gaps. This is called gap squeezing.

Data: The alignment in the box below contains a single gap in column 2, and all gaps in column 4.

Settings: The tolerance for gaps has been set to 100, so only column 4 will be removed ("squeezed") when you press the Run button.

Alignment:

a-t-gacgatcgat act-ggcgatcgat act-gacgatcgat gct-gacgatcgat

Options:

Gap character(s)	Tolerance for gaps (%)
Show deleted columns	Preserve deleted columns
Codons: delete columns in groups of 3	Reading frame of alignment: 1 2 3