-t filename Tree file (see Trees) - the program loads the tree from the given text file
--treenumber number Selects a tree from a file containing multiple trees.
-d filename Data file (see Data) - the program loads the sequence data from the given text file.
-f basefilename
family - both the tree and sequence file have the same name, but a
different file extension. The program attempts to locate both of them,
by testing the known extensions. [The possibilities are set at compile
time from fileExtensions.h. Hopefully later versions of
cold will allow the chosen file extensions to be set at
runtime. Also, hopefully, later versions will have improved detection
routines to help find the right files. For full details on the file
searching algorithms, see File Searching.]
--code code sets the genetic code to the one named. The genetic codes are given in the file geneticcodes. This file could be modified to add genetic codes if new codes are discovered, but it would also be necessary to provide new parametermatrices for the new codes. The default is universal code.
--codesfile filename sets the file filename for looking up genetic codes. This can be used to provide genetic codes not provided with COLD.