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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