clean up a messy MSA

You need to provide (1) a list of sequence names (fasta headers) that you trust in your alignment file, we would call them "Master sequences" and (2) the alignment file itself.
This program would not discard in-between unrelieble positions from your alignment. Rather, it will dicard
(a) all positions trailing beyond the start and end positions of the master sequences and
(b) all the sequences from your alignment file those have a gap at any positions where there is no gap in all the master sequences or have a base at any positions where all the master sequences have gaps.