Computing the Gamma Parameter (a)

In the computation of gamma distances, it is necessary to know the gamma parameter According to the gamma distribution, the substitution rate often varies from site to site within a sequence. The shape of this distribution is determined by a value known as the gamma parameter, which is also known as the shape parameter. (a).  This parameter may be estimated from the dataset under consideration or you may use the value obtained from previous studies.  For estimating a, a substantial number of sequences is necessary; if the number of sequences used is small, the estimate has a downward bias (Zhang and Gu 1998Zhang_and_Gu_1998).  The current release of MEGA does not contain any programs for estimating a; however we plan to make them available in the future.  Therefore you need to use another program for estimating the a value.  Some of the frequently used programs that include this facility are PAUP* (Swofford 1998Swofford_1998) for DNA sequences, PAML and PAMP programs for DNA and protein sequences (Yang 1999Yang_1999), and GAMMA programs from Gu and Zhang (1997)Gu_and_Zhang_1997.