-n number Number of iterations - this is the maximum number of iterations of Newton-Raphson to try while seeking to maximise likelihood. If the algorithm hasn't converged by the end of number iterations, it reports the current position, and does not delete the state file, so that execution can be resumed with the --recover option (see -recover). Unless the quiet flag is set, the output should be enough to indicate whether continuing would be likely to lead to convergence (i.e. if the value of number had been set too small).
--path searchpath sets the searchpath for all other files. See File Searching. This allows the user to store necessary data files in non-standard locations. The default searchpath is stored in the .variables file, and so can be changed.
[Later versions of Cold may allow this option to add to the search path, rather than replacing it.]
--simulate [number,]length[:seed] Simulates data: starting from the root of the tree, it simulates random evolution according to the model specified (using the other options, same as for maximising likelihood). The first number is the number of files to produce (the default is 1), and the second is the length of the sequences in each file (in nucleotides). This length should therefore be a multiple of 3 [there is currently no error checking for this]. If given, the seed is used to seed the random number generator. This makes it possible to reproduce the results. [The simulation uses the default random number generator provided by the compiler. This may not be good enough for some purposes.]
--freqs frequencies Sets the codon frequencies, either for use in optimisation, or for simulation.
--variableselect Automatically runs a crude variable selection algorithm. It checks the t-statistics after estimating the parameters. Any that are not significant are removed, and a new model is fitted on the remaining variables. If this model is significantly worse, the previous model is output. Otherwise, it looks at the t-statistics in the new model, and tries removing ones that are not significant.
This variable selection is rather crude, and it would probably be better to do the variable selection manually for individual data sets. This option is useful when selecting variables for many simulated data sets.
--state filename gives the name of the file to save the current state to if the program is interrupted, or has certain kinds of error. See State File. The file output is plain text, so it can be read by the user in the case of error, to help with debugging. The default filename is statefile.
[Bug: Currently, there is some problem with scaling, so that recovery does not work as expected.]
--recover filename tells the program to attempt to recover it's last state from a file, which should have been set using the --state option on a previous run, saving the need to repeat a lot of calculation.
--noautobackup By default, the program automatically backs up it's current position after every Newton-Raphson iteration, allowing some recovery in the event of an unstoppable interruption. This option disables automatic backups.