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:

seq1 a---ga-cgatcgat seq2 ac--gg-cgatcgat seq3 act-ga-cgatcgat seq4 gctaga-cgatcgat

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: 1 2 3
Reading frame of alignment: 1 2 3