BioPython - How do I align multiple sequences at once?

(This may be a really stupid question, but I cannot find what I'm looking for in the documentation)

I'm trying to align multiple sequences at once. From the biopython package, I can see how I can make an alignment of two sequences, e.g.:

from Bio.Seq import Seq 
from Bio import pairwise2

seq1 = Seq("ACCGGT") 
seq2 = Seq("ACGT")
alignments = pairwise2.align.globalxx(seq1, seq2)
print(alignments[0])

>>> Alignment(seqA='ACCGGT', seqB='A-C-GT', score=4.0, start=0, end=6) 

Which works fine.
Now I would like to align multiple sequences at once, altered from the docs:

from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Align import MultipleSeqAlignment
a = SeqRecord(Seq("AACGTAT"), id="Alpha")
b = SeqRecord(Seq("ACGTAT-"), id="Beta")
c = SeqRecord(Seq("AGGTAT-"), id="Gamma")
align = MultipleSeqAlignment([a, b, c],
                             annotations={"tool": "demo"},
                             column_annotations={"stats": "CCCXCCC"})
print(align)

>>> Alignment with 3 rows and 7 columns
AACGTAT Alpha
ACGTAT- Beta
AGGTAT- Gamma

But that does not really do anything. How do I now actually align these sequences?

in my env:

import Bio 

print('BIOPYTHON VERSION : ', Bio.__version__)


from Bio.Align.Applications import ClustalwCommandline

from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio import AlignIO

a = SeqRecord(Seq("AACGTAT"), id="Alpha")
b = SeqRecord(Seq("ACGTAT-"), id="Beta")
c = SeqRecord(Seq("AGGTAT-"), id="Gamma")


with open('input_clustal.fa', 'a') as handle:
    
    for i in [a,b,c]:
    
        SeqIO.write(i, handle ,'fasta')
        
        
clustalw_cline = ClustalwCommandline("./clustalw2", infile="input_clustal.fa")


print('clustal command : ', clustalw_cline)
print('--------------')



try : 
    
    a = clustalw_cline()
    
    print('ok')
    print('--------------')
    
    
    align = AlignIO.read("input_clustal.aln", "clustal")

    print(align)

    print('--------------')
     
    for i in range(len(align)):
        
        print(str(i+1)+'  ---> ', align[i].seq,'\n')

    
except Exception as E :
    
    print('Error : ', E)
    
    print('--------------')

output:

BIOPYTHON VERSION :  1.80
clustal command :  ./clustalw2 -infile=input_clustal.fa
--------------
ok
--------------
Alignment with 3 rows and 8 columns
AACGTAT- Alpha
-ACGTAT- Beta
-AGGTAT- Gamma
--------------
1  --->  AACGTAT- 

2  --->  -ACGTAT- 

3  --->  -AGGTAT- 

You need a clustalW executable on your machine like in example from:

http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec94

>>> import os
>>> from Bio.Align.Applications import ClustalwCommandline
>>> clustalw_exe = r"C:\Program Files\new clustal\clustalw2.exe"
>>> clustalw_cline = ClustalwCommandline(clustalw_exe, infile="opuntia.fasta")

As per from Bio.Align import MultipleSeqAlignment , MultipleSeqAlignment is just a Biopython Class (Object) that store a multiple sequences alignment and does not calculate it.

Remember to delete the input file created in from my code if you run the script more than once, otherwise you are feeding clustalw2 with same name sequrnces and that will throw an error:

BIOPYTHON VERSION :  1.80
clustal command :  ./clustalw2 -infile=input_clustal.fa
--------------
Error :  Non-zero return code 255 from './clustalw2 -infile=input_clustal.fa', message 'ERROR: Multiple sequences found with same name (found Alpha at least twice)!'
--------------