Are there any tools for mutational analysis of viruses?
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This is a very vague post. Have you already called SNPs, or this is what you want to do? If the latter, you can use standard variant callers like GATK, LoFreq, Mutect2, FreeBayes, etc... Choose whichever depending on requirements.
If you already have SNPs, you need to inform us with what kind of analysis you want to do.