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.