text: user6504: I have 6 viral genome sequences of the same virus and 1 reference sequence in FASTA format.
  
  How I can identify mutations and mutation sites in those genomes using FASTA sequences  but how I can do this for FASTA file?
  And how I can identify the mutation rate for one genome?
  
  Background If I've FASTQ file then I'll simply align the reads to the reference and by using variant calling tool I will get the mutate sites
  
  user8956: You can still align a FASTA file with a tool like bwa mem ( if they are short reads ) or minimap2 for long reads and run it through a variant caller like freebayes. Alternatively, if you have sufficient reads to create an assembly of all of the genomes, or if they already are you can create a MSA of them using a tool like Cactus (as it is built for genomes) or MAFFT if the sequences are short enough and then use your favorite viewer to find variable sites 
  
original_text: 6504: <p>I have 6 viral genome sequences of the same virus and 1 reference sequence in FASTA format.</p>
  <ol>
  <li>How I can identify mutations and mutation sites in those genomes using FASTA sequences  but how I can do this for FASTA file?</li>
  <li>And how I can identify the mutation rate for one genome?</li>
  </ol>
  <p><strong>Background</strong> If I've FASTQ file then I'll simply align the reads to the reference and by using variant calling tool I will get the mutate sites</p>
   8956: <p>You can still align a FASTA file with a tool like <a href="https://github.com/lh3/bwa" rel="nofollow noreferrer">bwa mem</a> ( if they are short reads ) or <a href="https://github.com/lh3/minimap2" rel="nofollow noreferrer">minimap2</a> for long reads and run it through a variant caller like <a href="https://github.com/ekg/freebayes" rel="nofollow noreferrer">freebayes</a>. Alternatively, if you have sufficient reads to create an assembly of all of the genomes, or if they already are you can create a MSA of them using a tool like <a href="https://github.com/ComparativeGenomicsToolkit/cactus" rel="nofollow noreferrer">Cactus</a> (as it is built for genomes) or MAFFT if the sequences are short enough and then use your favorite viewer to find variable sites </p>
  