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1.5 Output Options:

--output filename Saves the final output (see Output) to the file named filename. Without this option, Cold outputs this information to standard output (usually the screen).

--printsitelikes causes the program to print the likelihood for the data at each site, if the Newton-Raphson method converges, so that the maximum likelihood is found. If the optimisation does not converge (so the maximum likelihood is not found) this option does nothing.

--tstats causes the program to print t-statistics for all variables at the MLE (assuming it converges). These can be used to decide which variables are more likely to be important.

--observedinformation Causes the observed information matrix to be printed out in the final output. This matrix can be used to estimate asymptotic covariance.

--blstdev Outputs the estimated standard deviations of the branchlengths. These can be used to obtain confidence intervals for the branchlength estimates.