codonbias
This program will allow the user to estimate selection coefficients relating to optimal codon usage. The basic methodology is similar to the codon based models implemented in the popular program PAML by Ziheng Yang. However, it explicitly models selection for optimal codon usage on different lineages of a phylogeny. The program may be a bit hard to compile because it requires special libraries (see documentation). For any analysis which can also be done in PAML, we recommend using PAML as PAML is much superior to our program in a number of ways including ease of use, computational speed, how well it has been tested, etc.
