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pievos101 / PopGenome

An Efficient Swiss Army Knife for Population Genomic Analyses in R
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How do you specify a genetic code for analyses like MKT? #9

Open TeresaPegan opened 2 years ago

TeresaPegan commented 2 years ago

Hello! I would like to use the MKT function in PopGenome with a mitochondrial dataset. Because this involves assigning sites as synonymous or nonsynonymous, it is important for me to be able to specify that I need to use the vertebrate mitochondrial code, not the standard code. I cannot find a way to do this. Is it possible, or can this MKT function only be used on standard data? Thanks! -Teresa

abcdefghijklmn97 commented 2 years ago

Hello! I would like to use the MKT function in PopGenome with a mitochondrial dataset. Because this involves assigning sites as synonymous or nonsynonymous, it is important for me to be able to specify that I need to use the vertebrate mitochondrial code, not the standard code. I cannot find a way to do this. Is it possible, or can this MKT function only be used on standard data? Thanks! -Teresa

Hi,

I would like to ask if you have calculated MK?

Thanks!

TeresaPegan commented 2 years ago

Hi, no, I ended up using the python library egglib to calculate piN and piS, which is what I was mostly interested in. I was never able to figure out whether I could specify a mitochondrial genetic code with PopGenome.

abcdefghijklmn97 commented 2 years ago

Hi, no, I ended up using the python library egglib to calculate piN and piS, which is what I was mostly interested in. I was never able to figure out whether I could specify a mitochondrial genetic code with PopGenome.

Hi, Teresa

I need to calculate the McDonald Kreitman test, I looked at popGenome, to be honest I don't know how to calculate, my data volume is a bit large, and the genes are also a lot.

Thank you for your reply.

Best,

Jinhua Long