Codon Usage Programs

Codon Usage

In performing our research of genomes and genome evolution, we have created a variety of perl modules and programs. This includes the programs used in our work on modal codon usage:

Davis, J. J., and Olsen, G. J. 2009. Modal codon usage: Assessing the typical codon usage of a genome. Mol. Biol. Evol. 27: 800–810, Dec 17. [Epub ahead of print] (PubMed; MBE OpenAccess; doi: 10.1093/molbev/msp281; software).

Davis, J. J., and Olsen, G. J. 2010. Characterizing the native codon usages of a genome: An axis projection approach. Mol. Biol. Evol., Aug. 2. [Epub ahead of print] (PubMed; MBE OpenAccess; doi: 10.1093/molbev/msq185; software; examples).

The programs were developed and tested under Mac OS X 10.4 and 10.5, and should run with little or no modification on any unix-like system. The files are provided as a gzip tar file or a directory.

The current version is 1.00.

Download a gzip tar file with the current modal codon usage programs and libraries.

Download a gzip tar file containing a demonstration of making a tree from codon usage frequencies.

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Page written and maintained by Gary J. Olsen (gjo☮illinois.edu)