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:
a---ga-cgatcgat ac--gg-cgatcgat act-ga-cgatcgat gctaga-cgatcgat
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: 1 2 3
Reading frame of alignment: 1 2 3
Return to Gap Strip/Squeeze Input Page.