Kimura2Paramter to ks value/Time

oushujun / LTR_retriever

LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5813529/

GNU General Public License v3.0

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Kimura2Paramter to ks value/Time #170

Open manoharbisht1998 opened 2 months ago

manoharbisht1998 commented 2 months ago

Hi I have repeat landscape with Kimura2Parameter on x axis. I want to check the time of the burst of LTRs by using that repeat landscape. is there a way to convert the Kimura2Parameter values to time or ks value?

Thanks

oushujun commented 2 months ago

T = K/2u, where K is divergence which can be estimated using the K2P model. The default is the JC69 model. u is mutation rate (per bp per year).

manoharbisht1998 commented 2 months ago

Thank you for the answer. However, I have the repeat landscape (attached below) Screenshot (70) I want to calculate the insertion time. According to formula T =K/2u, isn't it similar to Ks time estimation; viz T=Ks/2u? Can we say that K2P value is equal to Ks?