6 Utilities included with Cold

The package also provides the following utility programs for converting files in formats not compatible with cold, into formats that can be used by the program:

• readmatricesfromcols: Read parametermatrices from a model matrix
• reordermatrix: Use matrices where codons are listed in a different order
• summats: Combine existing matrices to obtain new variables
• stripambiguous: Remove sites with ambiguous data.