# Removing degenerate characters

Degenerate IUPAC base symbols represent a site position that can have multiple possible characters. For a DNA example, “Y” represents pyrimidines where the site can be either “C” or “T”.

Note

In many molecular evolutionary and phylogenetic analyses, the gap character “-” is treated “N”, meaning any base.

Let’s create sample data with degenerate characters

## Omit aligned columns containing a degenerate character

## Omit all degenerate characters except gaps from an alignment

If we create the app with the argument `gap_is_degen=False`, we can omit degenerate characters but retain gaps.

## Omit k-mers which contain degenerate characters

If we create `omit_degenerates` with the argument `motif_length`, it will split sequences into non-overlapping tuples of the specified length and exclude any tuple that contains a degenerate character.

previous

Filtering data

next

Removing highly gapped positions