A description about the concept of codon usage bias is available at Wikipedia.
CodonW is software package written in C by John Peden with Paul Sharp. CodonW is designed for correspondence analysis of codon and amino acid usage. The description about CodonW is available through SourceForge. The webserver for CodonW is available at HERE.
This is a tool for visualizing codon usage frequency and covert codon usage frequency into relative adaptiveness values. The graphic codon usage analyzer webserver is avaialble at HERE.
JCAT is developed by Grote et al. for codon usage adaptation analysis. The implementation for CAI calculation is based on the algorithm described in Carbone et al. (2003). JCAT can perform CAI analyses for most prokaryotic organisms and selected eukaryotic organsims. JCAT considers additional options such as intrinic terminators and enzyme digestion sites into their analyses. The JCAT webserver is available HERE .
Codon Usage Database is developed by Yasukazu Nakamura with Toshimichi Ikemura for analyzing the codon usage frequency. This database contains codon usage frequencies for 2,298,913 complete protein coding genes in 32,775 organisms (March of 2007).
This page lists some useful information and tools for codon usage analysis that I know about. I am sure there will be more not included but this does not mean they are not important or with poor quality. This page will be updated regulatory. If you think I missed some, please contact us through e-mail wan@cvm.msstate.edu or wanhenry@yahoo.com to be listed. Thanks!