You can use Edit | Remove Gaps to remove gaps from a single protein or DNA sequence, a contig, align to reference alignment or a multiple sequence alignment.
The action does depend on which editor is currently open.
This command is enabled when some sequence has been selected and the sequence is unlocked.
Single Sequence (NA or AA): gaps are stripped from the current selection.
MSA (NA or AA): Gaps are stripped from the current selection. All MSA sequences must be the same length in the editor, so the ends may be padded with "aaps", but there will be no internal gaps in the selected region.
Align to Reference: If the Reference is selected in a reference contig then the gaps are removed from the reference and the corresponding residues in the Reads are deleted - those residues may be "real" residues, but the aim of this is to "clean up" the assembly and remove extraneous residues from the reads that are causing gaps to be inserted in the reference.
Assembler: For a regular reference Contig, the behaviour is the same as the Align to Reference Editor. For de novo contigs the behaviour is based on the consensus sequence instead of the reference.
If a read or section of a read is selected, then gaps are removed from that, which will likely disturb the alignment.