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Example of Intermediate Gap Tolerance

Goal: You want to remove from your alignment all columns that are more than 25% gaps. This is an operation intermediate between stripping and squeezing.

Data: The alignment in the box below contains a single gap in column 2, two gaps in column 3, three gaps in column 4, and all gaps in column 7.

Settings: The tolerance for gaps has been set to 26%, so that column 2, with 25% gaps (1 gap in 4 sequences) will be preserved. Columns 3, 4, and 7 will be removed because they exceed the 26% tolerance level specified when you press the Run button.

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 13:09 2013


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

 
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