I'm following the instructions for the "hard & slow" way to run RAxML as described in the User guide: https://cme.h-its.org/exelixis/resource/download/NewManual.pdf
I made 5 separate seed trees, and I'm testing out different parameters for the -i and -c values for each of the trees. I was wondering how I should be comparing the resulting likelihood values?
1) what exactly do these values represent? Are they likelihood values or log likelihood values?
2) what criteria do I use to compare two trees based on these likelihood values? (do I look at the 2*(log likelihood difference), and how do I assess statistical significance? or does it not matter and I only need to choose the smaller value?)
Thanks for taking the time