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Example of Preserving Removed Columns

Goal: You want to remove columns from an alignment but preserve an indication of which columns were removed. In this way you can preview what the Gap Strip/Squeeze operation has done to your alignment, and perhaps run the job again with different parameter settings.

Data: The alignment in the box below is in table format and contains differing numbers of gaps in various columns.

Settings: The tolerance for gaps has been set to 26%. In addition, the button marked "Preserve deleted columns" has been selected.

Alignment:

Options:

Gap character(s)

Tolerance for gaps (%)

Show deleted columns

Preserve 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 13:04 2013


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

 
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