13
((KF,(VV,((GM,(FS,(MD,PP))),(PG,((TC,AT),(PT,(CF,ptg))))))),CS);
Error: Only bounds for the root age are implemented..
I got the output file. But there is no tree.
Here is my mcmctree.ctl file:
seed = -1
seqfile = /$PWD/beast.fasta
treefile = /$PWD/tree
outfile = mcmctree_output
ndata = 1 * indicates there is only one dataset
seqtype = 2 * amino acids
clock = 2 * independent rates
RootAge = '<1.0' * safe constraint on root age, used if no fossil for root.
model = 6 * JTT substitution model
alpha = 0 * alpha for gamma rates at sites
ncatG = 5 * No. categories in discrete gamma
cleandata = 1
BDparas = 1 1 0.1 * birth, death, sampling
kappa_gamma = 6 2 * gamma prior for kappa
alpha_gamma = 1 1 * gamma prior for alpha
rgene_gamma = 2 20 1 * gammaDir prior for rate for genes
sigma2_gamma = 1 10 1 * gammaDir prior for sigma^2 (for clock=2 or 3)
finetune = 1: .1 .1 .1 .1 .1 .1 * auto (0 or 1) : times, rates, mixing...
print = 1 * 0: no mcmc sample; 1: everything except branch 2: ev...
burnin = 2000
I want to use default values since I don't know what is the RootAge for the analysis.
Anyone could help me to fix this error?
Thanks so much!