How to calculate pairwise ts/tv ratio given a alignment
Hi Everyone
Could anyone tell me how to calculate pairwise ts/tv ratio given a alignment (the 4-fold degenerate sites extracted from a CDS alignment)? which software or script can do this?
One example for the alignment (fasta) is like:
>taxa001
TATATATTTTTTTTAAAAATAATAATATTA
>taxa002
TATATATTCTTACTAAAAATAATAATATTA
>taxa003
TATATATTCTTACTAAAAATAATAATATTA
>taxa004
TATATATTCTTACTAAAAATAATAATATTA
>taxa005
TATATATTTTTTTTAAAAATAATAATATTA
>taxa006
TATATATTCTTACTAAAAATAATAATATTA
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Can you define what you mean by "alignments?" Typically for NGS data you're going to pull ts/tv from the variant (VCF) data.
The alignment is the 4-fold degenerate sites extracted from a CDS alignment
Show us a sample please.
The alignment (fasta) is like: