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.