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?
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