To find amino acid substitution from fasta alignment

Question

[shwetamgr1]

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.

[mohammadhassanj]

https://www.applied-maths.com/tutorial/sequence-alignment-and-mutation-analysis

[shwetamgr1]

thanks, this method will itself align and search from the sequence. my concern is from aligned file. i have already msa file in fasta alignment format. i want to perform search on that.