`--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.