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 gapstreeze 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
Codons: delete columns in groups of 3	Reading frame of alignment: 1 2 3