I am looking for a file format for specifying colours to be used when
displaying amino acids in a multiple protein alignment.
Programs such as JMol appear to hard-code these colours. Are there any
formats for existing programs that read colour schemes from a file?
I am writing a multiple sequence alignment editor and would like to be
able to read in many different colour schemes from files. For example
one colour scheme for hydrophobic vs. hydrophilic residues, and another
for secondary structure.
I would rather use an existing format than create a new one.