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Example Gap Strip

Goal: You want to remove all columns from your alignment that contain one or more gaps. This is called gap stripping.

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 zero, so both these columns will be removed ("stripped") when you press the Run button and leave the 'Preserve codons' checkbox unchecked.
2. If 'Preserve codons' is checked and you set both, the number of tolerance positions and the reading frame to 1 then the first two codons will be stripped.
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) is stripped.

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 13:52 2013


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

 
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