Notes on Yang & dos Reis 2000 MBE branch-site model

Statistical Properties of the Branch-Site Test of Positive Selection, Ziheng Yang and Mario dos Rei, 2000, MBE

what is foreground w2 and background?
w2 in the foreground branch are often infinite and unreliable.

It is sometimesattemptedtousetheestimateofx2asameasure
of the strength of selection in the gene on the foreground
branch.As discussed by Bakewell et al. (2007) and Nozawaet al.
(2009a), point estimates of x2 produced by the codeml program
are often infinite and unreliable.

References

Nozawa M, Suzuki Y, Nei M. 2009a. Reliabilities of identifying
positive selection by the branch-site and the site-prediction
methods. Proc Natl Acad Sci U S A. 106:6700–6705.


Bakewell MA, Shi P, Zhang J. 2007. More genes underwent positive
selection in chimpanzee evolution than in human evolution.
Proc Natl Acad Sci U S A. 104:7489–7494.