Linkage disequilibrium in Human Mitochondrial genome

Question

[Pramod Shinde]

I am working on human mitochondrial sequences of both healthy and disease origin. Could you please suggest any tools/Softwares to measure Linkage disequilibrium among these sequences.

Thanks in advance.

[Asaf]

But there is no recombination

Answer 1

[Asaf]

Disclaimer: I don't know how this is usually done but this is what I would do:

Since it's mitochondria you can actually build a phylogenetic tree of the genomes you have using a set of SNPs. Once you have the tree it's pretty simple to try to correlate each SNP (or other variant) with the disease state using BayesTraits, you're simply comparing two discrete variables so use discrete mode.