yn00 is a part of the PAML package, which is a suite of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood (ML).

yn00 implements the method of Yang and Nielsen (2000) for estimating synonymous and nonsynonymous substitution rates in pairwise comparison of protein-coding DNA sequences.

Most programs in the PAML package have control files that specify the names of the sequence data file, the tree structure file, and models and options for the analysis. The default control files are baseml.ctl for baseml and basemlg, codeml.ctl for codeml, pamp.ctl for pamp, mcmctree.ctl for mcmctree.

The progam evolver does not have a control file, and uses a simple user interface. All you do is to type evolver and then choose the options. For other programs, you should prepare a sequence data file and a tree structure file, and modify the appropriate control files before running the programs.

References:
Adachi, J., and M. Hasegawa. 1996a. MOLPHY Version 2.3: Programs for molecular phylogenetics based o�n maximum likelihood. Computer science monographs, 28:1-150. Institute of Statistical Mathematics, Tokyo.

Adachi, J., and M. Hasegawa. 1996b. Model of amino acid substitution in proteins encoded by mitochondrial DNA. Journal of Molecular Evolution 42:459-468.[Entrez]

Brown, W. M., E. M. Prager, A. Wang, and A. C. Wilson. 1982. Mitochondrial DNA sequences of primates, tempo and mode of evolution. Journal of Molecular Evolution 18:225-239.[Entrez]