Question: Linkage disequilibrium in Human Mitochondrial genome
gravatar for Pramod Shinde
16 months ago by
La Jolla Institute for Immunology
Pramod Shinde0 wrote:

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.

ADD COMMENTlink modified 16 months ago by Asaf8.4k • written 16 months ago by Pramod Shinde0

But there is no recombination

ADD REPLYlink written 16 months ago by Asaf8.4k
gravatar for Asaf
16 months ago by
Asaf8.4k wrote:

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.

ADD COMMENTlink written 16 months ago by Asaf8.4k
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