How to calculate pairwise ts/tv ratio given a alignment

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9.0 years ago

YMTIO • 0

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

substitution software alignment • 2.7k views

ADD COMMENT • link updated 22 months ago by Ram 43k • written 9.0 years ago by YMTIO • 0

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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.

ADD REPLY • link 9.0 years ago by Dan D 7.4k

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The alignment is the 4-fold degenerate sites extracted from a CDS alignment

ADD REPLY • link updated 22 months ago by Ram 43k • written 9.0 years ago by YMTIO • 0

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Show us a sample please.

ADD REPLY • link updated 22 months ago by Ram 43k • written 9.0 years ago by Pierre Lindenbaum 161k

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The alignment (fasta) is like:

>taxa001
TATATATTTTTTTTAAAAATAATAATATTA
>taxa002
TATATATTCTTACTAAAAATAATAATATTA
>taxa003
TATATATTCTTACTAAAAATAATAATATTA
>taxa004
TATATATTCTTACTAAAAATAATAATATTA
>taxa005
TATATATTTTTTTTAAAAATAATAATATTA
>taxa006
TATATATTCTTACTAAAAATAATAATATTA

ADD REPLY • link updated 22 months ago by Ram 43k • written 9.0 years ago by YMTIO • 0

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