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I have 6 viral genome sequences of the same virus and 1 reference sequence in FASTA format. I want to know, how I can identify mutations and mutation sites in those genomes using FASTA sequences (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) but how I can do this for FASTA file? And how I can identify the mutation rate for one genome?

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  • $\begingroup$ 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). $\endgroup$ – Kamil S Jaron Jun 8 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 at 0:54
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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

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  • $\begingroup$ 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. $\endgroup$ – Dr Animo Jun 4 at 3:30
  • $\begingroup$ And how I can calculate mutation rates? $\endgroup$ – Dr Animo Jun 4 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 $\endgroup$ – Nicholas Heyer Jun 5 at 20:20

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