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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:

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:

Reading frame of alignment:

Return to Gap Strip/Squeeze Input Page.

last modified: Thu Dec 12 13:49 2013


Questions or comments? Contact us at seq-info@lanl.gov.

 
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