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:
1. The tolerance for gaps has been set to 100, so only column 4 will be removed ("squeezed") when you press the Run button.
2. If 'Preserve codons' is checked and you set both, the number of tolerance positions and the reading frame to 1 then the second codon will be removed.
3. If 'Preserve codons' is checked and you set the number of tolerance positions to 1 but change the reading frame to 2, then the first codon (starting at position 2) will be removed.

Alignment:

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

Options:

Gap character(s)	Tolerance for gaps (%)
Show deleted columns
Preserve codons (delete columns in groups of 3)	Use tolerance for [1,2,3] positions in the codon: 1 2 3
Reading frame of alignment: 1 2 3