-
Notifications
You must be signed in to change notification settings - Fork 40
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Kimura2Paramter to ks value/Time #170
Comments
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). |
Yes, K2P is one of the popular ways to estimate K. Be aware that your K may be the estimated divergence from the given library sequences that may not represent the ancestral sequence of the TE family, thus the calculated T may be not equal to the insertion time of that TE sequence. |
@manoharbisht1998 Can you please let me know the method you used to calculate the K2P distance? I want to add an option to give K2P values for intact LTR elements in the output. |
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
The text was updated successfully, but these errors were encountered: