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Software

Synonymous likelihood analysis presented in Nielsen et al 2007 (Mol. Biol. Evol. 24: 228-235)
http://cteg.berkeley.edu/software.html

GOF analysis associated with selective sweeps presented in Jensen et al 2005 (Genetics 170: 1401-1410)

Correlated Evolution analysis as presented in Clark and Aquadro (2010). Download HyPhy scripts.

E-mail Vanessa Bauer DuMont (vlb2@cornell.edu) to receive the program to perform the counting "per site" method of synonymous site evolution presented in Bauer DuMont et al 2004 (Genetics 167: 171-185)