hii
Thank you for developing this tools, its really handy and best things is we can know what model we are running by plotting quickly.
I had few questions, currently i am working for non-modal organims, so i dont know ne size, but i do have mutation rate.
Intially, i filtered vcf for quality and then removed protein coding regions and kept only neutral regions for rest of analysis.
everyhting is running fine, but the size of Ne in intiall model, infleunce my divergence parameter, so how i can know which Ne to use, i have done PSMC and GONE analysis, can i use estimate from them.
I understand from your previous post, that Ne is number of generation it takes for two sample to find common ancestar, so how i can know, and if i am getting right Ne or how i can validate that ?
besides this i followed the tutorials and understand that f4,f3 can be used for goodness of fit, but can i get the value of observed and expected likelihood of given data and model, or some kind of relations ?
Besides this, i understand ghostpopulation can be modelled as example in tutorials, but it merge to one existing population, how we can merge it to ancestral population of all, like i had two population, which merge at t_div, and ghost population merge before that t_div_2, i tried but it always say root should be 1 populations.
I look forward for your guidance.
Thank you.
hii
Thank you for developing this tools, its really handy and best things is we can know what model we are running by plotting quickly.
I had few questions, currently i am working for non-modal organims, so i dont know ne size, but i do have mutation rate.
Intially, i filtered vcf for quality and then removed protein coding regions and kept only neutral regions for rest of analysis.
everyhting is running fine, but the size of Ne in intiall model, infleunce my divergence parameter, so how i can know which Ne to use, i have done PSMC and GONE analysis, can i use estimate from them.
I understand from your previous post, that Ne is number of generation it takes for two sample to find common ancestar, so how i can know, and if i am getting right Ne or how i can validate that ?
besides this i followed the tutorials and understand that f4,f3 can be used for goodness of fit, but can i get the value of observed and expected likelihood of given data and model, or some kind of relations ?
Besides this, i understand ghostpopulation can be modelled as example in tutorials, but it merge to one existing population, how we can merge it to ancestral population of all, like i had two population, which merge at t_div, and ghost population merge before that t_div_2, i tried but it always say root should be 1 populations.
I look forward for your guidance.
Thank you.