Hello everyone :)

I am running Beta-psmc with and without bootstrapping. When I plot the psmc without bootstrapping the Ne line goes up to ~10^5 years ago, but with the bootstrapping it recovers Ne up to ~10^7 years ago. I did not change any of the user specifications neither during the psmc itself (apart from adding bootstraps) nor during the plotting. Tried to change the maximum generations (-X option) but that only changed the x axis range not the range of psmc Ne estimates. Do you know what may be causing this difference in the temporal range of Ne estimation?

Sample images: Sample images:

With Bootstraps: https://ibb.co/BH4Q5sfB

Without bootstraps https://ibb.co/0jKj2JR0

Commands: Beta-psmc (no boots):

Beta-PSMC-master/beta-psmc -N25 -t15 -r5 -p 20*1 -B3 -o ${FILE[$SLURM_ARRAY_TASK_ID]}.final.beta.psmc ${FILE[$SLURM_ARRAY_TASK_ID]}.psmcfa

Beta-osmc (with boots):

seq 100 | xargs -P 6 -i echo psmc -N25 -t15 -r5 -b -p "20*1" -o round-{}.${FILE[$SLURM_ARRAY_TASK_ID]}.psmc ${FILE[$SLURM_ARRAY_TASK_ID]}.split.psmcfa | sh

cat ${FILE[$SLURM_ARRAY_TASK_ID]}.final.beta.psmc round-*${FILE[$SLURM_ARRAY_TASK_ID]}*psmc > ${FILE[$SLURM_ARRAY_TASK_ID]}.combined.boot.beta.psmc

Plotting (same for with and without bootstrapping:

../Beta-PSMC-master/utils/psmc_plot.pl
-g 1
-u 2.2e-9
-M "name1, name2"
-p all_in_one_plot_beta
name1 name2 etc