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Example: "Ambiguity" Gap Strip

Goal: Your alignment contains IUPAC ambiguity codes "r" meaning A or G, and "y" meaning C or T. You want to remove all columns from your alignment that contain one or more of the ambiguity codes and one or more gaps.

Data: The alignment in the box below contains ambiguity code "r" column 1, and "y" in column 7. There are also gaps in various columns.

Settings: The tolerance for gaps is set to zero, and in addition r and y are entered as gap characters in the "gap characters" box. Columns 1, 2, 4, and 7 will be removed 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 GapStreeze Input Page.

last modified: Thu Dec 12 13:44 2013


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