1 Invoking Cold

cold - Codon Optimal Likelihood Discoverer

cold calculates and maximises log-likelihoods for user-defined codon models in phylogeny.

This manual is for version 1.0.0 of cold

cold has a number of command line options as detailed below. A number of the options read input from files. The required formats of these files are described in See File Format. The options have been divided into the following categories

• Model Options: these control the model that the program fits to the data;
• Data Options: these control the data and tree on which the program fits the model;
• Starting Options: these control the initial estimate - these should not affect the final answer but could speed up the program, or avoid local maxima;
• Output Options: these control the final output of the program.
• Running Options: these control what the program outputs, how long it runs for, whether it backs up data while running, etc.;
• Debugging and Status Options: these control what the program prints on the screen while running (status updates, debugging information, etc.)
• Technical Options: these control the internal working of the program, and are mostly useful for debugging (only the -T option might be regularly useful for ordinary users).