suppose the running of jmodeltest2 come up the best model for my nucleotide alignment is as follow:
Best model = 010231+I+G+F
f(a) = 0.24
f(c) = 0.41
f(g) = 0.26
f(t) = 0.09
Percentage of invariable site = 0.18
Gamma = 0.52
Kappa = 0.09
Ra = 0.00
Rb = 0.396
Rc = 1.000
Rd = 0.396
Re = 0.479
Rf = 2.170
I would like to use this information to construct maximum likelihood in PhyML, and neighbour-joining tree in phylip. What parameters should I set for such running? I know it is a very fundamental question to ask. Thank you in advance.
Best regards
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