Extract Di-nucleotide/Tri-Nucleotide substitution frequencies from MSA/VCF file

Question

[Saran]

Hello,

I have 3 samples of Viral sequences for three different time points. Each sample has 100+ Near-full length HIV sequences (~8000 bp). I have remove the sequences with deletions and have only the intact viral sequences.

I would like to get the substitution frequency of dinucleotides & trinucleotides for each sample. I have previously found the SNP substitution frequency using VCFstats package (https://pwwang.github.io/vcfstats/).

Are there any available algorithms to extract this information from either a Multi-Seq Alignment or VCF file?

Thanks, Sara

[Pierre Lindenbaum]

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