clear
clf
rand('seed',17)

% === Parameters ===
nu= 0.9
Ntopos=3; % Number of topology states
rateFactorVector= [0.001,0.003,0.01,0.03,0.1,0.3,1,3,10,100];
Nrates= length(rateFactorVector)
NburnIn=100;
Nsample=200;
flag_updateNu=1
save_loglik=1;

% ------ Data ---------
data=LoadDNA('dataNeisseria.dat'); 

% ------ Simu ---------
Results=Barge_runMCMC(data,'NburnIn',NburnIn,'Nsample',Nsample,'rateFactorVector',rateFactorVector,'flag_updateNu',flag_updateNu,'nuRates',nu,'nuTopos',nu,'save_loglik',save_loglik);

% ------ Figures --------
Barge_PlotResults(Results);