remove-alignment-gaps <species> <alignment>
Remove from an alignment all columns that contain a gap in the specified species.
The name of a species present in the alignment for which gaps should be removed.
A DNA or protein sequence alignment in clustalw format. The alignment can be read from standard input if a "-" is given instead of a file name.
The alignment, with the remaining columns that don't have gaps in the specified species, is written to standard output.