MSA (protein) with biopython or something else?
In my personal experience, MUSCLE is the easiest program to use in conjunction with Biopython. Biopython features a command line wrapper for this program, which makes it very easy to use. Make sure to download the appropriate MUSCLE program from drive5 and save it somewhere. E.g., if you are using Jupyter in Linux:
!wget https://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_i86linux64.tar.gz
!tar -xzvf muscle3.8.31_i86linux64.tar.gz
!cp muscle3.8.31_i86linux64 /usr/local/bin
!chmod 755 /usr/local/bin/muscle3.8.31_i86linux64

Then, you can run MUSCLE like so:
from Bio.Align.Applications import MuscleCommandline
def runMUSCLE(infile, outfile):
    muscle_exe = r&quot;/usr/local/bin/muscle3.8.31_i86linux64&quot; #Here is where we installed MUSCLE
    muscle_cline = MuscleCommandline(muscle_exe,
                                     input=infile,
                                     out=outfile,
                                     clwstrict=True #Output in clustal format (more visually pleasing), otherwise the output is in FASTA. Whichever you need.
                                    )
    muscle_cline()

You don't need to specify that your sequence is amino acidic, however keep in mind that the input file must be in FASTA format.