DNArates is a program for estimating site-specific nucleotide substitution rates by maximum likelihood from an alignment of nucleotide sequences and a corresponding phylogenetic tree. This program grew out of the problem of supplying rate categories for the fastDNAml program and Felsenstein's DNAML program, consequently DNArates incorporates nucleotide substitution models and code from these programs.
The DNArates program has not yet been formally published, and should be cited as "Olsen, G. J., Pracht, S., and Overbeek, R., unpublished". However, it has been mentioned in publications (e.g., Maidak, B. L., Larsen, N., McCaughey, M. J., Overbeek, R., Olsen, G. J., Fogel, K., Blandy, J., and Woese, C. R. 1994. The Ribosomal Database Project. Nucleic Acids Res. 22: 3485–3487. (PubMed; PubMed Central)).
The directory DNArates contains the current release of the program and documentation files.
Gary
Return to Programs PagePage written and maintained by Gary J. Olsen (gjo☮illinois.edu)