The final output format can be specified completely with an output template (see Output Templates). This section describes the default output format.
If the --variableselect option (see -variableselect) is used, the first line of the output indicates which parameters have been selected.
The first line of final output states whether the Newton-Raphson method converged. If it converged, then the output is likely to be the maximum likelihood. If not, then the program did not find the maximum likelihood [but can be told to continue, using the state file]. In either case, the program then outputs either the MLE, or where it has currently searched to.
The next line of output is the inferred branch lengths in Newick format, but without the terminating semicolon.
If the --blstdev option (see -blstdev) is used, the next output is another tree in Newick format, with the estimated standard deviations for the estimated branch lengths. These can be used to give confidence intervals for branch lengths, but are not very reliable [often they are too large to be of much use].
Next is a table, listing for each parameter the coefficient in the COLD model (...), and the exponential of the coefficient (which is the parameter in some models.
If the --printsitelikes option (see -printsitelikes) is used, the next output is a table of the likelihoods for each site.
If the --tstats option (see -tstats) is used, the next output is a table of the t-statistics for each variable.
If the --observedinformation option (see -observedinformation) is given, then the final output is the observed information matrix. This can be used to give confidence intervals for parameter estimates.