How to iterate protein sequences using amino acids?
In response to question 1, save the following as a python3 script (e.g., aln_parser.py):

#!/usr/bin/env python3    

from Bio import AlignIO
import sys

aln = sys.argv[1]

algnmnt = AlignIO.read(open(aln, 'r'), 'clustal')

for col in range(0, algnmnt.get_alignment_length()):
    proteins = set(algnmnt[:,col])
    if len(proteins) == 1:
        print(f"Postion {col}: protein {''.join(proteins)}")


Run the script to query your alignment (clustal.aln).

python3 aln_parser.py clustal.aln

To save the output to file:

python3 aln_parser.py clustal.aln &gt; results.txt

Requires python3 and Biopython (pip3 install biopython).