text: user17079: I have fasta multiple sequence alignment file of protein sequence. I want to look for mutation/substitution in amino acid between query with reference to one query. Is there any R package or any method I can go through.
  
  user4401: User-friendly alternative:
  Get the alignment into Jalview, set a colour scheme you like, and inspect alignment visually. You can move sequences up and down in the alignment with keyboard arrows, so you can focus on what you need.
  Online, no-install-needed alternative:
  (same program as M_'s method)
  blastn on NCBI website. Tick 'align two or more sequences'. Query in the top box, all the others in the bottom box.
  (Would not use this method if you had> 20 seqences).
  If you have many sequences, I reccomend going with M_ 's advice instead.
  
original_text: 17079: <p>I have fasta multiple sequence alignment file of protein sequence. I want to look for mutation/substitution in amino acid between query with reference to one query. Is there any R package or any method I can go through.</p>
   4401: <p>User-friendly alternative:</p>
  <p>Get the alignment into Jalview, set a colour scheme you like, and inspect alignment visually. You can move sequences up and down in the alignment with keyboard arrows, so you can focus on what you need.</p>
  <p>Online, no-install-needed alternative:
  (same program as M_'s method)
  blastn on NCBI website. Tick 'align two or more sequences'. Query in the top box, all the others in the bottom box.
  (Would not use this method if you had&gt; 20 seqences).</p>
  <p>If you have many sequences, I reccomend going with M_ 's advice instead.</p>
  