29) Removing sequences that are fully gapped from alignment using BioEdit

Let’s say you have an alignment that looks like this after you cleaved out a particular region from a longer protein:
We intend to remove sequences that are fully gapped, as shown in red box above.

To do this,

1. Click on: Sequence >> Filter out sequences containing certain characters >> Cut them to new alignment


2. Select Contain non- and type “-“ in the textbox.
   This means we are asking the tool to extract any sequence that contains a non-gap character.

The sequences that are not fully gapped will be extracted to a new alignment, preserving the order of the sequences in the original alignment.

3. Save the output as a new .aln file, and you’ll have an alignment file without the fully gapped sequences!