I am trying to see how the effective population changes over time for a species. The generation time is about 4 and they live about 15 years. Plus they have a different mutation rate. What parameters should I change from default ? I read the documentation on github but I am still unsure.
The output of the binary psmc is in the so called 2N scale, which is irrelevant to the mutation rate and generation time. You do not need to worry about the two parameters when you run the binary - in fact, you will find that no psmc options are related to those. Mutation rate and generation time affect plotting the real scale. You only need to change the two parameters when plotting using psmc_plot.pl.
Sorry. I was not clear. You can change -p and other parameters, but you will note that there are no parameters related to generation time and mutation rate. I have modified my answer accordingly.
Thanks ! I am just wondering why the example on the website ( -p "4+252+4+6" ) differs from the default parameters (4+53+4).
Sorry. I was not clear. You can change -p and other parameters, but you will note that there are no parameters related to generation time and mutation rate. I have modified my answer accordingly.
I am sorry if I just interrupting the topic discussed above.
Can I know how to scale down Y axis (effective population size)?
The scale generated on my PSMC plot is too big and the changes in effective population size across time was unable to estimate.
You can modify scale using -Y parameter in plotting script from psmc/utils