# Removing highly gapped positions

Using the `omit_gap_pos` app, we can remove position from an alignment which exceed a specified proportions of gaps.

Let’s create a sample alignment with gaps.

## Removing highly gapped nucleotide positions

Sites with over 99% gaps are excluded by default.

We can alter the threshold for the allowed fraction of gaps with the `allowed_frac` argument. Let’s create an app that excludes all aligned sites with over 49% gaps.

## Removing highly gapped codon positions

To eliminate any codon columns (where a column is a triple of nucleotides) that contain a gap character, we use the `motif_length` argument.

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Removing degenerate characters

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Remove problem sequences from an alignment