title: Multiple sequence alignment by MUSCLE
body: <p>I want to do multiple sequence alignment by using MUSCLE algorithm .</p>
  
  <pre><code>from Bio.Align.Applications import MuscleCommandline
  muscle_exe = r"C:\Program file\muscle3.8.31_i86win32.exe"
  in_file = r"non_aligned.fasta"
  out_file = r"aligned.fasta"
  muscle_cline = MuscleCommandline(muscle_exe, input=in_file, out=out_file)
  print(muscle_cline)
  stdout, stderr = muscle_cline()
  </code></pre>
  
  <p>But, I want to use it in a different way as the following:</p>
  
  <pre><code>nsequences = len(sequences)
  
  for i in range(nsequences):
    for j in range(i+1, nsequences):
      aln = alignment_function(sequences[i], sequences[j])
     print (sequences[i], sequences[j], aln)
  </code></pre>
  
  <p>where <strong>sequences</strong> are the sequences contained in the file <strong>non_aligned.fasta</strong>, and <strong>nsequences</strong> is the number of sequences.
  So, I want to align two sequences by <strong>MUSCLE</strong> , each time like I mentioned in the above code and print every two sequences.
   <strong>alignment_function(sequences[i], sequences[j])</strong> is a function, which does the alignment of two sequences by <strong>MUSCLE</strong>. How can I do this ? This should then output something like:</p>
  
  <pre><code>seq1 seq2 aln12
  seq1 seq3 aln13
  seq2 seq3 aln23
  </code></pre>