I have 6 viral genome sequences of the same virus and 1 reference sequence in FASTA format.

  1. How I can identify mutations and mutation sites in those genomes using FASTA sequences but how I can do this for FASTA file?
  2. 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

  • $\begingroup$ The mutation rate is impossible to calculate without knowing when the samples diverged. If you have fasta sequences, you can align them and build a tree (I guess beast is the most common tool for viral genomes including time calibration). $\endgroup$ Jun 8, 2020 at 13:04
  • $\begingroup$ Typically you can align FASTA or FASTQ sequences. If your variant caller of choice doesn't accept a FASTA and you trust the bases in your FASTA you could mock up the quality scores and make a FASTQ $\endgroup$
    – Bioathlete
    Jun 11, 2020 at 0:54

1 Answer 1


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

  • $\begingroup$ I've assembled genome and the genome size is about 30-32k, so I align them and after that, I try to check variable region, It will take a lot of time. $\endgroup$
    – Mendel
    Jun 4, 2020 at 3:30
  • $\begingroup$ And how I can calculate mutation rates? $\endgroup$
    – Mendel
    Jun 4, 2020 at 3:39
  • $\begingroup$ I don't expect it to take too long to run as MAFFT i-INS-n ( mush slower then Cactus but probably more accurate) can align my dateset of 208 seq at 200kb in around 20000 clock hours (20 hrs with 10 cores ) so 6 should be fine unless they are really gappy. I am unclear what you mean about mutation rates in this context unless these genomes have established time points $\endgroup$ Jun 5, 2020 at 20:20

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